From 2c7a801d11b9366a398742a64c03980538b35c24 Mon Sep 17 00:00:00 2001 From: GitHub Actions Bot Date: Thu, 16 Jan 2025 06:01:25 +0000 Subject: [PATCH] Hourly export update --- bugsigdb_signatures_genus_metaphlan.gmt | 17 ++++---- bugsigdb_signatures_genus_metaphlan_exact.gmt | 15 ++++--- bugsigdb_signatures_genus_ncbi.gmt | 17 ++++---- bugsigdb_signatures_genus_ncbi_exact.gmt | 15 ++++--- bugsigdb_signatures_genus_taxname.gmt | 17 ++++---- bugsigdb_signatures_genus_taxname_exact.gmt | 15 ++++--- bugsigdb_signatures_mixed_metaphlan.gmt | 22 +++++----- bugsigdb_signatures_mixed_ncbi.gmt | 22 +++++----- bugsigdb_signatures_mixed_taxname.gmt | 22 +++++----- bugsigdb_signatures_species_metaphlan.gmt | 17 ++++---- ...gdb_signatures_species_metaphlan_exact.gmt | 17 ++++---- bugsigdb_signatures_species_ncbi.gmt | 17 ++++---- bugsigdb_signatures_species_ncbi_exact.gmt | 17 ++++---- bugsigdb_signatures_species_taxname.gmt | 17 ++++---- bugsigdb_signatures_species_taxname_exact.gmt | 17 ++++---- file_size.csv | 1 + full_dump.csv | 42 +++++++++---------- 17 files changed, 154 insertions(+), 153 deletions(-) diff --git a/bugsigdb_signatures_genus_metaphlan.gmt b/bugsigdb_signatures_genus_metaphlan.gmt index 9ffb305f1..e7ce04cba 100644 --- a/bugsigdb_signatures_genus_metaphlan.gmt +++ b/bugsigdb_signatures_genus_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus @@ -5432,7 +5432,7 @@ bsdb:1225/12/2_Self-reported-educational-attainment:Subjects-from-wealthier-hous bsdb:1225/13/1_Social-interaction-measurement:Subjects-from-the-wealthier-households-based-on-social-factors_vs_Subjects-from-the-least-well-off-households-based-on-social-factors_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-households-based-on-social-factors_vs_Subjects-from-the-least-well-off-households-based-on-social-factors_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Brachyspirales|f__Brachyspiraceae|g__Brachyspira k__Bacteria|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter bsdb:1226/1/1_Response-to-diet:0.2%-MC2-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum bsdb:1226/2/1_Response-to-diet:0.2%-MN3-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum bsdb:1226/3/1_Response-to-diet:4%-MN3-Pyloric-caecum_vs_4%-CTR-Diet-Pyloric-caecum_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas @@ -5519,23 +5519,22 @@ bsdb:1232/3/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_D bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia bsdb:1237/3/1_Response-to-transplant:Fecal-samples-at-the-end-of-the-experiment(Week-12)_vs_Fecal-samples-baseline(Week-0)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella diff --git a/bugsigdb_signatures_genus_metaphlan_exact.gmt b/bugsigdb_signatures_genus_metaphlan_exact.gmt index 70568c291..a705dfd0d 100644 --- a/bugsigdb_signatures_genus_metaphlan_exact.gmt +++ b/bugsigdb_signatures_genus_metaphlan_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes @@ -4695,23 +4695,22 @@ bsdb:1232/3/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_D bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia bsdb:1237/3/1_Response-to-transplant:Fecal-samples-at-the-end-of-the-experiment(Week-12)_vs_Fecal-samples-baseline(Week-0)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Schaedlerella diff --git a/bugsigdb_signatures_genus_ncbi.gmt b/bugsigdb_signatures_genus_ncbi.gmt index aec092a0c..3a00d4ef8 100644 --- a/bugsigdb_signatures_genus_ncbi.gmt +++ b/bugsigdb_signatures_genus_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA 1654 1716 1301 162289 189330 33024 40544 2759736 1386 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA 100883 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 207244 2759736 @@ -5432,7 +5432,7 @@ bsdb:1225/12/2_Self-reported-educational-attainment:Subjects-from-wealthier-hous bsdb:1225/13/1_Social-interaction-measurement:Subjects-from-the-wealthier-households-based-on-social-factors_vs_Subjects-from-the-least-well-off-households-based-on-social-factors_UP NA 239759 816 375288 909656 bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-households-based-on-social-factors_vs_Subjects-from-the-least-well-off-households-based-on-social-factors_DOWN NA 239759 816 29521 157 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA 816 838 2974251 577309 1926672 909656 2527773 872 -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA 239934 239759 2527773 838 2974251 +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA 2527773 bsdb:1226/1/1_Response-to-diet:0.2%-MC2-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA 106589 963 1543705 bsdb:1226/2/1_Response-to-diet:0.2%-MN3-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA 106589 963 1543705 bsdb:1226/3/1_Response-to-diet:4%-MN3-Pyloric-caecum_vs_4%-CTR-Diet-Pyloric-caecum_UP NA 286 @@ -5519,23 +5519,22 @@ bsdb:1232/3/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_D bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA 816 bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA 469 1348911 216851 55968 286 bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA 239759 244127 572511 189330 84111 1407607 644652 209 459786 1263 1301 -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 1980681 1263 189330 28050 572511 1573535 33042 292632 841 580596 -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 1766253 239759 207244 102106 33042 1407607 2172 375288 1473205 40544 3025755 816 1678 84111 1485 572511 1348911 1470349 216851 644652 +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 572511 580596 1980681 33042 189330 1573535 28050 841 1263 292632 +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 1766253 239759 207244 816 1678 572511 1470349 1485 102106 1348911 33042 84111 216851 1407607 644652 2172 375288 1473205 40544 3025755 1506553 bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 1980681 bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1654 bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA 1980681 bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA 292632 -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 239759 1980681 207244 572511 -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1678 1485 946234 577309 3025755 +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 239759 207244 572511 1980681 +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1678 1485 946234 577309 3025755 1506553 bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA 1301 bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA 816 bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA 1301 -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA 1301 -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 1485 +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 816 bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 459786 1980681 572511 216851 841 1678 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 816 572511 189330 216851 946234 1407607 1573535 1506553 2759736 248744 3025755 bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 2759736 1654 1926677 102106 86331 1573535 117563 1980681 580596 248744 397864 216851 29465 572511 544 1678 28050 1505652 906 1766253 904 -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 33042 375288 40544 816 572511 207244 216851 1407607 3025755 239759 574697 1980681 459786 84108 +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 239759 207244 816 572511 574697 1980681 33042 216851 1407607 459786 375288 84108 40544 3025755 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 2759736 1654 1926677 102106 86331 1573535 117563 248744 580596 397864 216851 29465 572511 544 1678 28050 1505652 906 904 1766253 bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 239759 207244 816 572511 574697 1980681 33042 216851 1407607 459786 375288 40544 3025755 bsdb:1237/3/1_Response-to-transplant:Fecal-samples-at-the-end-of-the-experiment(Week-12)_vs_Fecal-samples-baseline(Week-0)_UP NA 2676048 diff --git a/bugsigdb_signatures_genus_ncbi_exact.gmt b/bugsigdb_signatures_genus_ncbi_exact.gmt index 97a1c94d8..662a76ed3 100644 --- a/bugsigdb_signatures_genus_ncbi_exact.gmt +++ b/bugsigdb_signatures_genus_ncbi_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA 1654 1716 1301 162289 189330 33024 40544 1386 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA 100883 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 207244 @@ -4695,23 +4695,22 @@ bsdb:1232/3/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_D bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA 816 bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA 469 1348911 216851 55968 286 bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA 239759 244127 572511 189330 84111 1407607 644652 209 459786 1263 1301 -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 1980681 1263 189330 28050 572511 1573535 33042 292632 841 580596 -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 1766253 239759 207244 102106 33042 1407607 2172 375288 1473205 40544 3025755 816 1678 84111 1485 572511 1348911 1470349 216851 644652 +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 572511 580596 1980681 33042 189330 1573535 28050 841 1263 292632 +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 1766253 239759 207244 816 1678 572511 1470349 1485 102106 1348911 33042 84111 216851 1407607 644652 2172 375288 1473205 40544 3025755 1506553 bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 1980681 bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1654 bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA 1980681 bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA 292632 -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 239759 1980681 207244 572511 -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1678 1485 946234 577309 3025755 +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 239759 207244 572511 1980681 +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1678 1485 946234 577309 3025755 1506553 bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA 1301 bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA 816 bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA 1301 -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA 1301 -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 1485 +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 816 bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 459786 1980681 572511 216851 841 1678 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 816 572511 189330 216851 946234 1407607 1573535 1506553 2759736 248744 3025755 bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 2759736 1654 1926677 102106 86331 1573535 117563 1980681 580596 248744 397864 216851 29465 572511 544 1678 28050 1505652 906 1766253 904 -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 33042 375288 40544 816 572511 207244 216851 1407607 3025755 239759 574697 1980681 459786 84108 +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 239759 207244 816 572511 574697 1980681 33042 216851 1407607 459786 375288 84108 40544 3025755 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 2759736 1654 1926677 102106 86331 1573535 117563 248744 580596 397864 216851 29465 572511 544 1678 28050 1505652 906 904 1766253 bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 239759 207244 816 572511 574697 1980681 33042 216851 1407607 459786 375288 40544 3025755 bsdb:1237/3/1_Response-to-transplant:Fecal-samples-at-the-end-of-the-experiment(Week-12)_vs_Fecal-samples-baseline(Week-0)_UP NA 2676048 diff --git a/bugsigdb_signatures_genus_taxname.gmt b/bugsigdb_signatures_genus_taxname.gmt index 85cf281a6..023b81003 100644 --- a/bugsigdb_signatures_genus_taxname.gmt +++ b/bugsigdb_signatures_genus_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA Actinomyces Corynebacterium Streptococcus Peptoniphilus Dorea Phascolarctobacterium Sutterella Lacticaseibacillus Bacillus bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA Coprobacillus bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Anaerostipes Lacticaseibacillus @@ -5432,7 +5432,7 @@ bsdb:1225/12/2_Self-reported-educational-attainment:Subjects-from-wealthier-hous bsdb:1225/13/1_Social-interaction-measurement:Subjects-from-the-wealthier-households-based-on-social-factors_vs_Subjects-from-the-least-well-off-households-based-on-social-factors_UP NA Alistipes Bacteroides Parabacteroides Phocaeicola bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-households-based-on-social-factors_vs_Subjects-from-the-least-well-off-households-based-on-social-factors_DOWN NA Alistipes Bacteroides Brachyspira Treponema bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA Bacteroides Prevotella Segatella Paraprevotella Prevotellamassilia Phocaeicola Candidatus Cibiobacter Desulfovibrio -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA Akkermansia Alistipes Candidatus Cibiobacter Prevotella Segatella +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA Candidatus Cibiobacter bsdb:1226/1/1_Response-to-diet:0.2%-MC2-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA Cupriavidus Herbaspirillum Nitrospirillum bsdb:1226/2/1_Response-to-diet:0.2%-MN3-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA Cupriavidus Herbaspirillum Nitrospirillum bsdb:1226/3/1_Response-to-diet:4%-MN3-Pyloric-caecum_vs_4%-CTR-Diet-Pyloric-caecum_UP NA Pseudomonas @@ -5519,23 +5519,22 @@ bsdb:1232/3/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_D bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA Bacteroides bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA Acinetobacter Coprobacter Faecalibacterium Leucobacter Pseudomonas bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA Alistipes Anaerotruncus Blautia Dorea Eggerthella Fusicatenibacter Gordonibacter Helicobacter Oscillibacter Ruminococcus Streptococcus -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Colidextribacter Ruminococcus Dorea Lachnospira Blautia Holdemanella Coprococcus Subdoligranulum Roseburia Butyricicoccus -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Agathobacter Alistipes Anaerostipes Collinsella Coprococcus Fusicatenibacter Methanobrevibacter Parabacteroides Senegalimassilia Sutterella Thomasclavelia Bacteroides Bifidobacterium Eggerthella Clostridium Blautia Coprobacter Candidatus Stoquefichus Faecalibacterium Gordonibacter +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Blautia Butyricicoccus Colidextribacter Coprococcus Dorea Holdemanella Lachnospira Roseburia Ruminococcus Subdoligranulum +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Agathobacter Alistipes Anaerostipes Bacteroides Bifidobacterium Blautia Candidatus Stoquefichus Clostridium Collinsella Coprobacter Coprococcus Eggerthella Faecalibacterium Fusicatenibacter Gordonibacter Methanobrevibacter Parabacteroides Senegalimassilia Sutterella Thomasclavelia Lachnoclostridium bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Colidextribacter bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Actinomyces bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA Colidextribacter bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA Subdoligranulum -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Alistipes Colidextribacter Anaerostipes Blautia -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Bifidobacterium Clostridium Flavonifractor Paraprevotella Thomasclavelia +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Alistipes Anaerostipes Blautia Colidextribacter +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Bifidobacterium Clostridium Flavonifractor Paraprevotella Thomasclavelia Lachnoclostridium bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA Streptococcus bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA Bacteroides bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA Streptococcus -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA Streptococcus -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Clostridium +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Bacteroides bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Oscillibacter Colidextribacter Blautia Faecalibacterium Roseburia Bifidobacterium bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Bacteroides Blautia Dorea Faecalibacterium Flavonifractor Fusicatenibacter Holdemanella Lachnoclostridium Lacticaseibacillus Marvinbryantia Thomasclavelia bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lacticaseibacillus Actinomyces Raoultibacter Collinsella Mogibacterium Holdemanella Granulicatella Colidextribacter Butyricicoccus Marvinbryantia Barnesiella Faecalibacterium Veillonella Blautia Citrobacter Bifidobacterium Lachnospira Terrisporobacter Megasphaera Agathobacter Acidaminococcus -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Coprococcus Parabacteroides Sutterella Bacteroides Blautia Anaerostipes Faecalibacterium Fusicatenibacter Thomasclavelia Alistipes Butyricimonas Colidextribacter Oscillibacter Slackia +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Alistipes Anaerostipes Bacteroides Blautia Butyricimonas Colidextribacter Coprococcus Faecalibacterium Fusicatenibacter Oscillibacter Parabacteroides Slackia Sutterella Thomasclavelia bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lacticaseibacillus Actinomyces Raoultibacter Collinsella Mogibacterium Holdemanella Granulicatella Marvinbryantia Butyricicoccus Barnesiella Faecalibacterium Veillonella Blautia Citrobacter Bifidobacterium Lachnospira Terrisporobacter Megasphaera Acidaminococcus Agathobacter bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Alistipes Anaerostipes Bacteroides Blautia Butyricimonas Colidextribacter Coprococcus Faecalibacterium Fusicatenibacter Oscillibacter Parabacteroides Sutterella Thomasclavelia bsdb:1237/3/1_Response-to-transplant:Fecal-samples-at-the-end-of-the-experiment(Week-12)_vs_Fecal-samples-baseline(Week-0)_UP NA Schaedlerella diff --git a/bugsigdb_signatures_genus_taxname_exact.gmt b/bugsigdb_signatures_genus_taxname_exact.gmt index 2b0243d46..3c911e0e6 100644 --- a/bugsigdb_signatures_genus_taxname_exact.gmt +++ b/bugsigdb_signatures_genus_taxname_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA Actinomyces Corynebacterium Streptococcus Peptoniphilus Dorea Phascolarctobacterium Sutterella Bacillus bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA Coprobacillus bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Anaerostipes @@ -4695,23 +4695,22 @@ bsdb:1232/3/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_D bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA Bacteroides bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA Acinetobacter Coprobacter Faecalibacterium Leucobacter Pseudomonas bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA Alistipes Anaerotruncus Blautia Dorea Eggerthella Fusicatenibacter Gordonibacter Helicobacter Oscillibacter Ruminococcus Streptococcus -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Colidextribacter Ruminococcus Dorea Lachnospira Blautia Holdemanella Coprococcus Subdoligranulum Roseburia Butyricicoccus -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Agathobacter Alistipes Anaerostipes Collinsella Coprococcus Fusicatenibacter Methanobrevibacter Parabacteroides Senegalimassilia Sutterella Thomasclavelia Bacteroides Bifidobacterium Eggerthella Clostridium Blautia Coprobacter Candidatus Stoquefichus Faecalibacterium Gordonibacter +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Blautia Butyricicoccus Colidextribacter Coprococcus Dorea Holdemanella Lachnospira Roseburia Ruminococcus Subdoligranulum +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Agathobacter Alistipes Anaerostipes Bacteroides Bifidobacterium Blautia Candidatus Stoquefichus Clostridium Collinsella Coprobacter Coprococcus Eggerthella Faecalibacterium Fusicatenibacter Gordonibacter Methanobrevibacter Parabacteroides Senegalimassilia Sutterella Thomasclavelia Lachnoclostridium bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Colidextribacter bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Actinomyces bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA Colidextribacter bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA Subdoligranulum -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Alistipes Colidextribacter Anaerostipes Blautia -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Bifidobacterium Clostridium Flavonifractor Paraprevotella Thomasclavelia +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Alistipes Anaerostipes Blautia Colidextribacter +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Bifidobacterium Clostridium Flavonifractor Paraprevotella Thomasclavelia Lachnoclostridium bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA Streptococcus bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA Bacteroides bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA Streptococcus -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA Streptococcus -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Clostridium +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Bacteroides bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Oscillibacter Colidextribacter Blautia Faecalibacterium Roseburia Bifidobacterium bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Bacteroides Blautia Dorea Faecalibacterium Flavonifractor Fusicatenibacter Holdemanella Lachnoclostridium Lacticaseibacillus Marvinbryantia Thomasclavelia bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lacticaseibacillus Actinomyces Raoultibacter Collinsella Mogibacterium Holdemanella Granulicatella Colidextribacter Butyricicoccus Marvinbryantia Barnesiella Faecalibacterium Veillonella Blautia Citrobacter Bifidobacterium Lachnospira Terrisporobacter Megasphaera Agathobacter Acidaminococcus -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Coprococcus Parabacteroides Sutterella Bacteroides Blautia Anaerostipes Faecalibacterium Fusicatenibacter Thomasclavelia Alistipes Butyricimonas Colidextribacter Oscillibacter Slackia +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Alistipes Anaerostipes Bacteroides Blautia Butyricimonas Colidextribacter Coprococcus Faecalibacterium Fusicatenibacter Oscillibacter Parabacteroides Slackia Sutterella Thomasclavelia bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lacticaseibacillus Actinomyces Raoultibacter Collinsella Mogibacterium Holdemanella Granulicatella Marvinbryantia Butyricicoccus Barnesiella Faecalibacterium Veillonella Blautia Citrobacter Bifidobacterium Lachnospira Terrisporobacter Megasphaera Acidaminococcus Agathobacter bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Alistipes Anaerostipes Bacteroides Blautia Butyricimonas Colidextribacter Coprococcus Faecalibacterium Fusicatenibacter Oscillibacter Parabacteroides Sutterella Thomasclavelia bsdb:1237/3/1_Response-to-transplant:Fecal-samples-at-the-end-of-the-experiment(Week-12)_vs_Fecal-samples-baseline(Week-0)_UP NA Schaedlerella diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt index a5b36f281..7795595ec 100644 --- a/bugsigdb_signatures_mixed_metaphlan.gmt +++ b/bugsigdb_signatures_mixed_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus k__Bacteria|p__Cyanobacteriota bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae @@ -6226,7 +6226,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM49-4BH k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AM28-29 k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium OM08-6BH k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AM59-24XD k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4 k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4 k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4 k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4 k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens bsdb:1226/1/1_Response-to-diet:0.2%-MC2-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum bsdb:1226/2/1_Response-to-diet:0.2%-MN3-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum bsdb:1226/3/1_Response-to-diet:4%-MN3-Pyloric-caecum_vs_4%-CTR-Diet-Pyloric-caecum_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas @@ -6331,23 +6331,23 @@ bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA k__Bac bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes k__Bacteria|k__Bacillati|p__Actinomycetota k__Bacteria|k__Bacillati|p__Bacillota k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes k__Bacteria|k__Bacillati|p__Actinomycetota k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus bsdb:1234/1/2_Freeze-dried-specimen:Freeze-dried-samples._vs_Frozen-samples_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|p__Lentisphaerota k__Bacteria|k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Pseudomonadati|p__Lentisphaerota k__Bacteria|k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae k__Bacteria|s__rumen bacterium NK4A214 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__uncultured Christensenellaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|s__rumen bacterium NK4A214 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Muricomes|s__Muricomes sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 14-2 diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt index 469255ac7..c04924724 100644 --- a/bugsigdb_signatures_mixed_ncbi.gmt +++ b/bugsigdb_signatures_mixed_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA 91061 1236 1654 1716 1301 162289 189330 33024 40544 2037 2049 506 186826 1300 31977 91347 1653 57037 1386 186817 bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA 100883 1117 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 207244 57037 @@ -6226,7 +6226,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA 158836 28052 74426 bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA 2292991 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA 1940789 817 33043 1871022 1602169 1680 46506 572010 2518605 1982626 39485 454154 1318 1150298 1852370 2293035 2292349 2292274 821 2500537 2293138 901 418240 2126740 253257 729 116085 1776391 39491 -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA 239935 1288121 2500537 2292206 2293015 1982626 2053569 2173 1519439 1602169 2518605 572010 +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA 239935 1288121 2500537 2292206 2293015 1982626 2053569 2173 52226 1519439 1602169 2518605 572010 bsdb:1226/1/1_Response-to-diet:0.2%-MC2-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA 106589 963 1543705 bsdb:1226/2/1_Response-to-diet:0.2%-MN3-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA 106589 963 1543705 bsdb:1226/3/1_Response-to-diet:4%-MN3-Pyloric-caecum_vs_4%-CTR-Diet-Pyloric-caecum_UP NA 80864 286 @@ -6331,23 +6331,23 @@ bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA 815 17 bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA 469 2037 1760 201174 1239 119060 186801 1348911 186802 216851 186803 55968 85023 468 216572 135621 72274 286 bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA 1760 201174 239759 244127 572511 186801 84107 84999 189330 84111 186802 1407607 644652 209 72293 186803 459786 216572 171550 1263 1300 1301 bsdb:1234/1/2_Freeze-dried-specimen:Freeze-dried-samples._vs_Frozen-samples_DOWN NA 990719 186803 216572 -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 290054 1980681 186826 1940338 331632 707003 1643826 438033 297314 39485 1263 189330 28050 572511 1573535 39492 33042 292632 42322 841 580596 186803 -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 1766253 239759 207244 102106 33042 1407607 2172 375288 1473205 40544 33039 256845 1906119 186803 297314 3025755 816 1678 84111 1485 572511 1348911 1470349 216851 644652 2005473 -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 1643826 1980681 707003 349920 186826 200644 290054 +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 572511 580596 1980681 33042 189330 1940338 42322 1573535 28050 39485 841 1263 438033 292632 39492 1643826 186803 186826 331632 297314 707003 +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 1766253 239759 207244 816 1678 572511 1470349 1485 102106 1348911 33042 84111 216851 1407607 644652 2172 375288 1473205 40544 3025755 33039 256845 1906119 186803 2005473 297314 1506553 +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 1980681 1643826 200644 186826 349920 707003 bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1654 186803 128827 877428 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA 1980681 1643826 290054 707003 200644 +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA 1980681 1643826 200644 707003 bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA 292632 707003 -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 239759 186826 1643826 1980681 290054 349920 207244 707003 33039 572511 -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1678 1906119 1485 946234 577309 3025755 186803 707003 +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 239759 207244 572511 1980681 33039 1643826 186826 349920 707003 +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 816 1678 1485 946234 577309 3025755 186803 707003 1906119 1506553 216572 bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA 1301 bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA 816 bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA 1301 -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA 1301 -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 1940338 1485 +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA 1306 +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 1506 816 bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 459786 1229255 1980681 297314 1522 572511 216851 841 877428 1678 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 816 572511 189330 216851 946234 1407607 1573535 1506553 2759736 248744 3025755 200644 186803 216572 297314 707003 bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 2759736 1654 216572 1926677 102106 86331 1573535 117563 1980681 580596 248744 397864 216851 29465 39485 572511 1940338 544 543 1678 28050 1505652 186803 906 1766253 904 -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 33042 375288 40544 816 572511 186803 207244 297314 216851 1407607 3025755 239759 574697 1980681 459786 707003 84108 33039 +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 239759 207244 816 572511 574697 1980681 33042 216851 1407607 459786 375288 84108 40544 3025755 33039 186803 297314 707003 423410 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 2759736 216572 1654 1926677 102106 86331 1573535 117563 248744 580596 397864 216851 29465 39485 572511 1940338 543 544 1678 28050 1505652 906 904 1766253 186803 bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 239759 207244 816 572511 574697 1980681 33042 216851 1407607 459786 375288 40544 3025755 33039 186803 297314 707003 bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA 2163169 1918608 397286 diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt index 77e48d1df..59810765d 100644 --- a/bugsigdb_signatures_mixed_taxname.gmt +++ b/bugsigdb_signatures_mixed_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA Bacilli Gammaproteobacteria Actinomyces Corynebacterium Streptococcus Peptoniphilus Dorea Phascolarctobacterium Sutterella Actinomycetales Actinomycetaceae Alcaligenaceae Lactobacillales Streptococcaceae Veillonellaceae Enterobacterales Corynebacteriaceae Lacticaseibacillus zeae Bacillus Bacillaceae bsdb:1/1/2_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_DOWN NA Coprobacillus Cyanobacteriota bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Anaerostipes Lacticaseibacillus zeae @@ -6226,7 +6226,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA Enterobacter hormaechei Lachnospira pectinoschiza Collinsella aerofaciens bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA Catenibacterium sp. AM22-15 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA Lactococcus petauri Bacteroides fragilis Coprococcus eutactus Parolsenella massiliensis Prevotella pectinovora Bifidobacterium adolescentis Bacteroides stercoris Slackia isoflavoniconvertens Segatella hominis Faecalibacillus intestinalis Lachnospira eligens Paraprevotella clara Streptococcus parasanguinis Fusicatenibacter saccharivorans Prevotellamassilia timonensis Clostridium sp. AM49-4BH Eubacterium sp. AM28-29 Clostridiaceae bacterium OM08-6BH Phocaeicola vulgatus Candidatus Cibiobacter qucibialis Roseburia sp. AM59-24XD Desulfovibrio piger Blautia wexlerae Clostridium fessum Lacrimispora amygdalina Haemophilus parainfluenzae Coprococcus catus Romboutsia timonensis Agathobacter rectalis -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA Akkermansia muciniphila Alistipes senegalensis Candidatus Cibiobacter qucibialis Clostridium sp. AF27-2AA Clostridium sp. AF36-4 Faecalibacillus intestinalis Lentisphaeria bacterium Methanobrevibacter smithii Oscillibacter sp. ER4 Prevotella pectinovora Segatella hominis Slackia isoflavoniconvertens +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA Akkermansia muciniphila Alistipes senegalensis Candidatus Cibiobacter qucibialis Clostridium sp. AF27-2AA Clostridium sp. AF36-4 Faecalibacillus intestinalis Lentisphaeria bacterium Methanobrevibacter smithii Mitsuokella multacida Oscillibacter sp. ER4 Prevotella pectinovora Segatella hominis Slackia isoflavoniconvertens bsdb:1226/1/1_Response-to-diet:0.2%-MC2-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA Cupriavidus Herbaspirillum Nitrospirillum bsdb:1226/2/1_Response-to-diet:0.2%-MN3-Diet-T2_vs_0.2%-CTR-Diet-T2_UP NA Cupriavidus Herbaspirillum Nitrospirillum bsdb:1226/3/1_Response-to-diet:4%-MN3-Pyloric-caecum_vs_4%-CTR-Diet-Pyloric-caecum_UP NA Comamonadaceae Pseudomonas @@ -6331,23 +6331,23 @@ bsdb:1233/1/1_Ketogenic-diet:treatment-group_vs_pre-treatment-group_UP NA Bacter bsdb:1233/1/2_Ketogenic-diet:treatment-group_vs_pre-treatment-group_DOWN NA Acinetobacter Actinomycetales Actinomycetes Actinomycetota Bacillota Burkholderiaceae Clostridia Coprobacter Eubacteriales Faecalibacterium Lachnospiraceae Leucobacter Microbacteriaceae Moraxellaceae Oscillospiraceae Pseudomonadaceae Pseudomonadales Pseudomonas bsdb:1233/2/1_Response-to-ketogenic-diet:non-responders_vs_responders_UP NA Actinomycetes Actinomycetota Alistipes Anaerotruncus Blautia Clostridia Coriobacteriaceae Coriobacteriales Dorea Eggerthella Eubacteriales Fusicatenibacter Gordonibacter Helicobacter Helicobacteraceae Lachnospiraceae Oscillibacter Oscillospiraceae Rikenellaceae Ruminococcus Streptococcaceae Streptococcus bsdb:1234/1/2_Freeze-dried-specimen:Freeze-dried-samples._vs_Frozen-samples_DOWN NA Christensenellaceae Lachnospiraceae Oscillospiraceae -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Eubacterium coprostanoligenes Colidextribacter Lactobacillales Escherichia/Shigella sp. uncultured Coriobacteriaceae bacterium uncultured Oscillospiraceae bacterium Eggerthellaceae Ruminococcus gauvreauii uncultured Lachnospiraceae bacterium Lachnospira eligens Ruminococcus Dorea Lachnospira Blautia Holdemanella [Eubacterium] siraeum Coprococcus Subdoligranulum Eubacterium ruminantium Roseburia Butyricicoccus Lachnospiraceae -bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Agathobacter Alistipes Anaerostipes Collinsella Coprococcus Fusicatenibacter Methanobrevibacter Parabacteroides Senegalimassilia Sutterella [Ruminococcus] torques Lentisphaerota Candidatus Gastranaerophilales Lachnospiraceae uncultured Lachnospiraceae bacterium Thomasclavelia Bacteroides Bifidobacterium Eggerthella Clostridium Blautia Coprobacter Candidatus Stoquefichus Faecalibacterium Gordonibacter Muribaculaceae -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Eggerthellaceae Colidextribacter uncultured Oscillospiraceae bacterium uncultured Coriobacteriales bacterium Lactobacillales Flavobacteriales Eubacterium coprostanoligenes +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Blautia Butyricicoccus Colidextribacter Coprococcus Dorea Escherichia/Shigella sp. Eubacterium ruminantium Holdemanella Lachnospira Lachnospira eligens Roseburia Ruminococcus Ruminococcus gauvreauii Subdoligranulum [Eubacterium] siraeum Eggerthellaceae Lachnospiraceae Lactobacillales uncultured Coriobacteriaceae bacterium uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium +bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Agathobacter Alistipes Anaerostipes Bacteroides Bifidobacterium Blautia Candidatus Stoquefichus Clostridium Collinsella Coprobacter Coprococcus Eggerthella Faecalibacterium Fusicatenibacter Gordonibacter Methanobrevibacter Parabacteroides Senegalimassilia Sutterella Thomasclavelia [Ruminococcus] torques Lentisphaerota Candidatus Gastranaerophilales Lachnospiraceae Muribaculaceae uncultured Lachnospiraceae bacterium Lachnoclostridium +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Colidextribacter Eggerthellaceae Flavobacteriales Lactobacillales uncultured Coriobacteriales bacterium uncultured Oscillospiraceae bacterium bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Actinomyces Lachnospiraceae Erysipelotrichaceae rumen bacterium NK4A214 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA Colidextribacter Eggerthellaceae Eubacterium coprostanoligenes uncultured Oscillospiraceae bacterium Flavobacteriales +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA Colidextribacter Eggerthellaceae Flavobacteriales uncultured Oscillospiraceae bacterium bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA Subdoligranulum uncultured Oscillospiraceae bacterium -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Alistipes Lactobacillales Eggerthellaceae Colidextribacter Eubacterium coprostanoligenes uncultured Coriobacteriales bacterium Anaerostipes uncultured Oscillospiraceae bacterium [Ruminococcus] torques Blautia -bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Bifidobacterium Candidatus Gastranaerophilales Clostridium Flavonifractor Paraprevotella Thomasclavelia Lachnospiraceae uncultured Oscillospiraceae bacterium +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Alistipes Anaerostipes Blautia Colidextribacter [Ruminococcus] torques Eggerthellaceae Lactobacillales uncultured Coriobacteriales bacterium uncultured Oscillospiraceae bacterium +bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA Bacteroides Bifidobacterium Clostridium Flavonifractor Paraprevotella Thomasclavelia Lachnospiraceae uncultured Oscillospiraceae bacterium Candidatus Gastranaerophilales Lachnoclostridium Oscillospiraceae bsdb:1235/5/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_UP NA Streptococcus bsdb:1235/5/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Entacapone-Low(ENT-Low)--after-6hours-of-incubation_DOWN NA Bacteroides bsdb:1235/6/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-6hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High)-and-Loxapine-Succinate-Low(LOX-Low)-after-6hours-of-incubation_UP NA Streptococcus -bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA Streptococcus -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Escherichia/Shigella sp. Clostridium +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA Streptococcus sp. +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Clostridium sp. Bacteroides bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Oscillibacter uncultured Christensenellaceae bacterium Colidextribacter uncultured Lachnospiraceae bacterium [Clostridium] innocuum Blautia Faecalibacterium Roseburia rumen bacterium NK4A214 Bifidobacterium bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Bacteroides Blautia Dorea Faecalibacterium Flavonifractor Fusicatenibacter Holdemanella Lachnoclostridium Lacticaseibacillus Marvinbryantia Thomasclavelia Flavobacteriales Lachnospiraceae Oscillospiraceae uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lacticaseibacillus Actinomyces Oscillospiraceae Raoultibacter Collinsella Mogibacterium Holdemanella Granulicatella Colidextribacter Butyricicoccus Marvinbryantia Barnesiella Faecalibacterium Veillonella Lachnospira eligens Blautia Escherichia/Shigella sp. Citrobacter Enterobacteriaceae Bifidobacterium Lachnospira Terrisporobacter Lachnospiraceae Megasphaera Agathobacter Acidaminococcus -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Coprococcus Parabacteroides Sutterella Bacteroides Blautia Lachnospiraceae Anaerostipes uncultured Lachnospiraceae bacterium Faecalibacterium Fusicatenibacter Thomasclavelia Alistipes Butyricimonas Colidextribacter Oscillibacter uncultured Oscillospiraceae bacterium Slackia [Ruminococcus] torques +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Alistipes Anaerostipes Bacteroides Blautia Butyricimonas Colidextribacter Coprococcus Faecalibacterium Fusicatenibacter Oscillibacter Parabacteroides Slackia Sutterella Thomasclavelia [Ruminococcus] torques Lachnospiraceae uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium Enterococcaceae bacterium RF39 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lacticaseibacillus Oscillospiraceae Actinomyces Raoultibacter Collinsella Mogibacterium Holdemanella Granulicatella Marvinbryantia Butyricicoccus Barnesiella Faecalibacterium Veillonella Lachnospira eligens Blautia Escherichia/Shigella sp. Enterobacteriaceae Citrobacter Bifidobacterium Lachnospira Terrisporobacter Megasphaera Acidaminococcus Agathobacter Lachnospiraceae bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA Alistipes Anaerostipes Bacteroides Blautia Butyricimonas Colidextribacter Coprococcus Faecalibacterium Fusicatenibacter Oscillibacter Parabacteroides Sutterella Thomasclavelia [Ruminococcus] torques Lachnospiraceae uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA Kineothrix sp. Muricomes sp. Lachnospiraceae bacterium 14-2 diff --git a/bugsigdb_signatures_species_metaphlan.gmt b/bugsigdb_signatures_species_metaphlan.gmt index db4b58be8..a643aa3ac 100644 --- a/bugsigdb_signatures_species_metaphlan.gmt +++ b/bugsigdb_signatures_species_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae @@ -2749,7 +2749,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM49-4BH k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AM28-29 k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium OM08-6BH k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AM59-24XD k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4 k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4 k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4 k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4 k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens bsdb:1229/1/1_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis bsdb:1229/1/2_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii bsdb:1229/2/1_Endometrial-cancer:High-Grade_vs_Benign_UP NA k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans @@ -2807,19 +2807,20 @@ bsdb:1232/2/1_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodonti bsdb:1232/2/2_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodontitis--Deep-pocket_vs_Healthy-controls_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum sp. oral taxon 183 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 169 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 175 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 877 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322 k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas oleovorans k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212 k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215 k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223 k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225 k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia trevisanii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 058 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 064 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 423 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis bsdb:1232/4/1_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_UP NA k__Bacteria|k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 135 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes bsdb:1232/4/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 175 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|s__rumen bacterium NK4A214 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__uncultured Christensenellaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum k__Bacteria|s__rumen bacterium NK4A214 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Muricomes|s__Muricomes sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 14-2 diff --git a/bugsigdb_signatures_species_metaphlan_exact.gmt b/bugsigdb_signatures_species_metaphlan_exact.gmt index db4b58be8..a643aa3ac 100644 --- a/bugsigdb_signatures_species_metaphlan_exact.gmt +++ b/bugsigdb_signatures_species_metaphlan_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae @@ -2749,7 +2749,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter hormaechei k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira pectinoschiza k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella aerofaciens bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM49-4BH k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AM28-29 k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium OM08-6BH k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AM59-24XD k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4 k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4 k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4 k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis k__Bacteria|k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4 k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens bsdb:1229/1/1_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas|s__Porphyromonas uenonis bsdb:1229/1/2_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus epidermidis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus agalactiae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Winkia|s__Winkia neuii bsdb:1229/2/1_Endometrial-cancer:High-Grade_vs_Benign_UP NA k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium ulcerans @@ -2807,19 +2807,20 @@ bsdb:1232/2/1_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodonti bsdb:1232/2/2_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodontitis--Deep-pocket_vs_Healthy-controls_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinobaculum|s__Actinobaculum sp. oral taxon 183 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces gerencseriae k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces johnsonii k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces massiliensis k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces naeslundii k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 169 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 175 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 877 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia|s__Arachnia propionica k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Bergeyella|s__Bergeyella sp. oral taxon 322 k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter showae k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga haemolytica k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga sputigena k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium hominis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium|s__Cardiobacterium valvarum k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium durum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Ectopseudomonas|s__Ectopseudomonas oleovorans k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Eikenella|s__Eikenella corrodens k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium periodonticum k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium polymorphum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella morbillorum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum|s__Lachnoanaerobaculum umeaense k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia buccalis k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hofstadii k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia hongkongensis k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 212 k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 215 k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 223 k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia sp. oral taxon 225 k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia|s__Leptotrichia trevisanii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria mucosa k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Pseudoleptotrichia|s__Pseudoleptotrichia goodfellowii k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia dentocariosa k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia mucilaginosa k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus australis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus cristatus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus gordonii k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus infantis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus intermedius k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sanguinis k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 058 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 064 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 423 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. oral taxon 431 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus vestibularis k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella|s__Veillonella parvula k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter|s__Campylobacter gracilis bsdb:1232/4/1_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_UP NA k__Bacteria|k__Pseudomonadati|p__Spirochaetota|c__Spirochaetia|o__Spirochaetales|f__Treponemataceae|g__Treponema|s__Treponema socranskii k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella uli k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|s__Veillonellaceae bacterium oral taxon 135 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia exigua k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister|s__Dialister pneumosintes bsdb:1232/4/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella adiacens k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces sp. oral taxon 175 k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus mitis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas|s__Stenotrophomonas maltophilia -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|s__rumen bacterium NK4A214 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp. +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__uncultured Christensenellaceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum k__Bacteria|s__rumen bacterium NK4A214 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp. bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Muricomes|s__Muricomes sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 14-2 diff --git a/bugsigdb_signatures_species_ncbi.gmt b/bugsigdb_signatures_species_ncbi.gmt index 34d9c5477..59b1f349a 100644 --- a/bugsigdb_signatures_species_ncbi.gmt +++ b/bugsigdb_signatures_species_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA 57037 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 57037 bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA 57037 @@ -2749,7 +2749,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA 158836 28052 74426 bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA 2292991 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA 1940789 817 33043 1871022 1602169 1680 46506 572010 2518605 1982626 39485 454154 1318 1150298 1852370 2293035 2292349 2292274 821 2500537 2293138 901 418240 2126740 253257 729 116085 1776391 39491 -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA 239935 1288121 2500537 2292206 2293015 1982626 2053569 2173 1519439 1602169 2518605 572010 +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA 239935 1288121 2500537 2292206 2293015 1982626 2053569 2173 52226 1519439 1602169 2518605 572010 bsdb:1229/1/1_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_UP NA 1506 281920 bsdb:1229/1/2_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_DOWN NA 1282 1311 33007 bsdb:1229/2/1_Endometrial-cancer:High-Grade_vs_Benign_UP NA 861 @@ -2807,19 +2807,20 @@ bsdb:1232/2/1_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodonti bsdb:1232/2/2_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodontitis--Deep-pocket_vs_Healthy-controls_DOWN NA 46125 712888 52769 544581 461393 1655 712116 712119 1227263 1750 712187 204 45243 1019 2718 194702 61592 301 539 860 76857 1379 29391 84135 46124 729 505 617123 47671 40542 157688 554406 712357 712359 712363 671213 109328 488 157692 172042 2047 43675 40324 113107 45634 1302 68892 1338 28037 1305 712622 712624 712632 712633 1343 29466 824 bsdb:1232/4/1_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_UP NA 53419 133926 713067 84109 39950 bsdb:1232/4/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_DOWN NA 1379 46124 712119 28037 40324 -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 290054 1940338 331632 707003 438033 297314 39485 39492 42322 +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 1940338 42322 39485 438033 39492 331632 297314 707003 bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 33039 297314 -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 707003 349920 290054 +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 349920 707003 bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 877428 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA 290054 707003 +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA 707003 bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA 707003 -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 290054 349920 707003 33039 +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 33039 349920 707003 bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 707003 -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 1940338 +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA 1306 +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 1506 bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 1229255 297314 1522 877428 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 297314 707003 bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 39485 1940338 -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 297314 707003 33039 +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 33039 297314 707003 423410 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 39485 1940338 bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 33039 297314 707003 bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA 2163169 1918608 397286 diff --git a/bugsigdb_signatures_species_ncbi_exact.gmt b/bugsigdb_signatures_species_ncbi_exact.gmt index 34d9c5477..59b1f349a 100644 --- a/bugsigdb_signatures_species_ncbi_exact.gmt +++ b/bugsigdb_signatures_species_ncbi_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA 57037 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 57037 bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA 57037 @@ -2749,7 +2749,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA 158836 28052 74426 bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA 2292991 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA 1940789 817 33043 1871022 1602169 1680 46506 572010 2518605 1982626 39485 454154 1318 1150298 1852370 2293035 2292349 2292274 821 2500537 2293138 901 418240 2126740 253257 729 116085 1776391 39491 -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA 239935 1288121 2500537 2292206 2293015 1982626 2053569 2173 1519439 1602169 2518605 572010 +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA 239935 1288121 2500537 2292206 2293015 1982626 2053569 2173 52226 1519439 1602169 2518605 572010 bsdb:1229/1/1_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_UP NA 1506 281920 bsdb:1229/1/2_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_DOWN NA 1282 1311 33007 bsdb:1229/2/1_Endometrial-cancer:High-Grade_vs_Benign_UP NA 861 @@ -2807,19 +2807,20 @@ bsdb:1232/2/1_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodonti bsdb:1232/2/2_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodontitis--Deep-pocket_vs_Healthy-controls_DOWN NA 46125 712888 52769 544581 461393 1655 712116 712119 1227263 1750 712187 204 45243 1019 2718 194702 61592 301 539 860 76857 1379 29391 84135 46124 729 505 617123 47671 40542 157688 554406 712357 712359 712363 671213 109328 488 157692 172042 2047 43675 40324 113107 45634 1302 68892 1338 28037 1305 712622 712624 712632 712633 1343 29466 824 bsdb:1232/4/1_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_UP NA 53419 133926 713067 84109 39950 bsdb:1232/4/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_DOWN NA 1379 46124 712119 28037 40324 -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 290054 1940338 331632 707003 438033 297314 39485 39492 42322 +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 1940338 42322 39485 438033 39492 331632 297314 707003 bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 33039 297314 -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 707003 349920 290054 +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 349920 707003 bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 877428 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA 290054 707003 +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA 707003 bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA 707003 -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 290054 349920 707003 33039 +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA 33039 349920 707003 bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA 707003 -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 1940338 +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA 1306 +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA 1506 bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 1229255 297314 1522 877428 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 297314 707003 bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 39485 1940338 -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 297314 707003 33039 +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 33039 297314 707003 423410 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA 39485 1940338 bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA 33039 297314 707003 bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA 2163169 1918608 397286 diff --git a/bugsigdb_signatures_species_taxname.gmt b/bugsigdb_signatures_species_taxname.gmt index 40a8d359e..8a4af4f1a 100644 --- a/bugsigdb_signatures_species_taxname.gmt +++ b/bugsigdb_signatures_species_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA Lacticaseibacillus zeae bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Lacticaseibacillus zeae bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA Lacticaseibacillus zeae @@ -2749,7 +2749,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA Enterobacter hormaechei Lachnospira pectinoschiza Collinsella aerofaciens bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA Catenibacterium sp. AM22-15 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA Lactococcus petauri Bacteroides fragilis Coprococcus eutactus Parolsenella massiliensis Prevotella pectinovora Bifidobacterium adolescentis Bacteroides stercoris Slackia isoflavoniconvertens Segatella hominis Faecalibacillus intestinalis Lachnospira eligens Paraprevotella clara Streptococcus parasanguinis Fusicatenibacter saccharivorans Prevotellamassilia timonensis Clostridium sp. AM49-4BH Eubacterium sp. AM28-29 Clostridiaceae bacterium OM08-6BH Phocaeicola vulgatus Candidatus Cibiobacter qucibialis Roseburia sp. AM59-24XD Desulfovibrio piger Blautia wexlerae Clostridium fessum Lacrimispora amygdalina Haemophilus parainfluenzae Coprococcus catus Romboutsia timonensis Agathobacter rectalis -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA Akkermansia muciniphila Alistipes senegalensis Candidatus Cibiobacter qucibialis Clostridium sp. AF27-2AA Clostridium sp. AF36-4 Faecalibacillus intestinalis Lentisphaeria bacterium Methanobrevibacter smithii Oscillibacter sp. ER4 Prevotella pectinovora Segatella hominis Slackia isoflavoniconvertens +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA Akkermansia muciniphila Alistipes senegalensis Candidatus Cibiobacter qucibialis Clostridium sp. AF27-2AA Clostridium sp. AF36-4 Faecalibacillus intestinalis Lentisphaeria bacterium Methanobrevibacter smithii Mitsuokella multacida Oscillibacter sp. ER4 Prevotella pectinovora Segatella hominis Slackia isoflavoniconvertens bsdb:1229/1/1_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_UP NA Clostridium sp. Porphyromonas uenonis bsdb:1229/1/2_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_DOWN NA Staphylococcus epidermidis Streptococcus agalactiae Winkia neuii bsdb:1229/2/1_Endometrial-cancer:High-Grade_vs_Benign_UP NA Fusobacterium ulcerans @@ -2807,19 +2807,20 @@ bsdb:1232/2/1_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodonti bsdb:1232/2/2_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodontitis--Deep-pocket_vs_Healthy-controls_DOWN NA Abiotrophia defectiva Actinobaculum sp. oral taxon 183 Actinomyces gerencseriae Actinomyces johnsonii Actinomyces massiliensis Actinomyces naeslundii Actinomyces sp. oral taxon 169 Actinomyces sp. oral taxon 175 Actinomyces sp. oral taxon 877 Arachnia propionica Bergeyella sp. oral taxon 322 Campylobacter showae Capnocytophaga haemolytica Capnocytophaga sputigena Cardiobacterium hominis Cardiobacterium valvarum Corynebacterium durum Ectopseudomonas oleovorans Eikenella corrodens Fusobacterium periodonticum Fusobacterium polymorphum Gemella haemolysans Gemella morbillorum Gemella sanguinis Granulicatella adiacens Haemophilus parainfluenzae Kingella oralis Lachnoanaerobaculum umeaense Lautropia mirabilis Leptotrichia buccalis Leptotrichia hofstadii Leptotrichia hongkongensis Leptotrichia sp. oral taxon 212 Leptotrichia sp. oral taxon 215 Leptotrichia sp. oral taxon 223 Leptotrichia sp. oral taxon 225 Leptotrichia trevisanii Neisseria mucosa Pseudoleptotrichia goodfellowii Rothia aeria Rothia dentocariosa Rothia mucilaginosa Stenotrophomonas maltophilia Streptococcus australis Streptococcus cristatus Streptococcus gordonii Streptococcus infantis Streptococcus intermedius Streptococcus mitis Streptococcus sanguinis Streptococcus sp. oral taxon 058 Streptococcus sp. oral taxon 064 Streptococcus sp. oral taxon 423 Streptococcus sp. oral taxon 431 Streptococcus vestibularis Veillonella parvula Campylobacter gracilis bsdb:1232/4/1_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_UP NA Treponema socranskii Olsenella uli Veillonellaceae bacterium oral taxon 135 Slackia exigua Dialister pneumosintes bsdb:1232/4/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_DOWN NA Gemella haemolysans Granulicatella adiacens Actinomyces sp. oral taxon 175 Streptococcus mitis Stenotrophomonas maltophilia -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Eubacterium coprostanoligenes Escherichia/Shigella sp. uncultured Coriobacteriaceae bacterium uncultured Oscillospiraceae bacterium Ruminococcus gauvreauii uncultured Lachnospiraceae bacterium Lachnospira eligens [Eubacterium] siraeum Eubacterium ruminantium +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Escherichia/Shigella sp. Eubacterium ruminantium Lachnospira eligens Ruminococcus gauvreauii [Eubacterium] siraeum uncultured Coriobacteriaceae bacterium uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA [Ruminococcus] torques uncultured Lachnospiraceae bacterium -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA uncultured Oscillospiraceae bacterium uncultured Coriobacteriales bacterium Eubacterium coprostanoligenes +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA uncultured Coriobacteriales bacterium uncultured Oscillospiraceae bacterium bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA rumen bacterium NK4A214 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA Eubacterium coprostanoligenes uncultured Oscillospiraceae bacterium +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA uncultured Oscillospiraceae bacterium bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA uncultured Oscillospiraceae bacterium -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Eubacterium coprostanoligenes uncultured Coriobacteriales bacterium uncultured Oscillospiraceae bacterium [Ruminococcus] torques +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA [Ruminococcus] torques uncultured Coriobacteriales bacterium uncultured Oscillospiraceae bacterium bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA uncultured Oscillospiraceae bacterium -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Escherichia/Shigella sp. +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA Streptococcus sp. +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Clostridium sp. bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA uncultured Christensenellaceae bacterium uncultured Lachnospiraceae bacterium [Clostridium] innocuum rumen bacterium NK4A214 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lachnospira eligens Escherichia/Shigella sp. -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium [Ruminococcus] torques +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA [Ruminococcus] torques uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium Enterococcaceae bacterium RF39 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lachnospira eligens Escherichia/Shigella sp. bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA [Ruminococcus] torques uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA Kineothrix sp. Muricomes sp. Lachnospiraceae bacterium 14-2 diff --git a/bugsigdb_signatures_species_taxname_exact.gmt b/bugsigdb_signatures_species_taxname_exact.gmt index 40a8d359e..8a4af4f1a 100644 --- a/bugsigdb_signatures_species_taxname_exact.gmt +++ b/bugsigdb_signatures_species_taxname_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_16:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA Lacticaseibacillus zeae bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Lacticaseibacillus zeae bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA Lacticaseibacillus zeae @@ -2749,7 +2749,7 @@ bsdb:1225/13/2_Social-interaction-measurement:Subjects-from-the-wealthier-househ bsdb:1225/14/1_Environmental-factor:Subjects-from-wealthier-households-based-on-village-factors_vs_Subjects-from-the-least-well-off-households-based-on-village-factors_UP NA Enterobacter hormaechei Lachnospira pectinoschiza Collinsella aerofaciens bsdb:1225/15/1_Water:Subjects-from-wealthier-households-based-on-water-sources_vs_Subjects-from-the-least-well-off-households-based-on-water-sources_UP NA Catenibacterium sp. AM22-15 bsdb:1225/16/1_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_UP NA Lactococcus petauri Bacteroides fragilis Coprococcus eutactus Parolsenella massiliensis Prevotella pectinovora Bifidobacterium adolescentis Bacteroides stercoris Slackia isoflavoniconvertens Segatella hominis Faecalibacillus intestinalis Lachnospira eligens Paraprevotella clara Streptococcus parasanguinis Fusicatenibacter saccharivorans Prevotellamassilia timonensis Clostridium sp. AM49-4BH Eubacterium sp. AM28-29 Clostridiaceae bacterium OM08-6BH Phocaeicola vulgatus Candidatus Cibiobacter qucibialis Roseburia sp. AM59-24XD Desulfovibrio piger Blautia wexlerae Clostridium fessum Lacrimispora amygdalina Haemophilus parainfluenzae Coprococcus catus Romboutsia timonensis Agathobacter rectalis -bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA Akkermansia muciniphila Alistipes senegalensis Candidatus Cibiobacter qucibialis Clostridium sp. AF27-2AA Clostridium sp. AF36-4 Faecalibacillus intestinalis Lentisphaeria bacterium Methanobrevibacter smithii Oscillibacter sp. ER4 Prevotella pectinovora Segatella hominis Slackia isoflavoniconvertens +bsdb:1225/16/2_Lifestyle-measurement:Phenotypes-with-strain-phylogenetic-information_vs_Phenotypes-without-strain-phylogenetic-information_DOWN NA Akkermansia muciniphila Alistipes senegalensis Candidatus Cibiobacter qucibialis Clostridium sp. AF27-2AA Clostridium sp. AF36-4 Faecalibacillus intestinalis Lentisphaeria bacterium Methanobrevibacter smithii Mitsuokella multacida Oscillibacter sp. ER4 Prevotella pectinovora Segatella hominis Slackia isoflavoniconvertens bsdb:1229/1/1_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_UP NA Clostridium sp. Porphyromonas uenonis bsdb:1229/1/2_Endometrial-cancer:Tumor-(Low-Grade-+-High-Grade)_vs_Benign_DOWN NA Staphylococcus epidermidis Streptococcus agalactiae Winkia neuii bsdb:1229/2/1_Endometrial-cancer:High-Grade_vs_Benign_UP NA Fusobacterium ulcerans @@ -2807,19 +2807,20 @@ bsdb:1232/2/1_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodonti bsdb:1232/2/2_Aggressive-periodontitis:Grade-C(previously-aggressive)-Periodontitis--Deep-pocket_vs_Healthy-controls_DOWN NA Abiotrophia defectiva Actinobaculum sp. oral taxon 183 Actinomyces gerencseriae Actinomyces johnsonii Actinomyces massiliensis Actinomyces naeslundii Actinomyces sp. oral taxon 169 Actinomyces sp. oral taxon 175 Actinomyces sp. oral taxon 877 Arachnia propionica Bergeyella sp. oral taxon 322 Campylobacter showae Capnocytophaga haemolytica Capnocytophaga sputigena Cardiobacterium hominis Cardiobacterium valvarum Corynebacterium durum Ectopseudomonas oleovorans Eikenella corrodens Fusobacterium periodonticum Fusobacterium polymorphum Gemella haemolysans Gemella morbillorum Gemella sanguinis Granulicatella adiacens Haemophilus parainfluenzae Kingella oralis Lachnoanaerobaculum umeaense Lautropia mirabilis Leptotrichia buccalis Leptotrichia hofstadii Leptotrichia hongkongensis Leptotrichia sp. oral taxon 212 Leptotrichia sp. oral taxon 215 Leptotrichia sp. oral taxon 223 Leptotrichia sp. oral taxon 225 Leptotrichia trevisanii Neisseria mucosa Pseudoleptotrichia goodfellowii Rothia aeria Rothia dentocariosa Rothia mucilaginosa Stenotrophomonas maltophilia Streptococcus australis Streptococcus cristatus Streptococcus gordonii Streptococcus infantis Streptococcus intermedius Streptococcus mitis Streptococcus sanguinis Streptococcus sp. oral taxon 058 Streptococcus sp. oral taxon 064 Streptococcus sp. oral taxon 423 Streptococcus sp. oral taxon 431 Streptococcus vestibularis Veillonella parvula Campylobacter gracilis bsdb:1232/4/1_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_UP NA Treponema socranskii Olsenella uli Veillonellaceae bacterium oral taxon 135 Slackia exigua Dialister pneumosintes bsdb:1232/4/2_Aggressive-periodontitis:GCP--Deep-pocket_vs_GCP--Shallow-pocket_DOWN NA Gemella haemolysans Granulicatella adiacens Actinomyces sp. oral taxon 175 Streptococcus mitis Stenotrophomonas maltophilia -bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Eubacterium coprostanoligenes Escherichia/Shigella sp. uncultured Coriobacteriaceae bacterium uncultured Oscillospiraceae bacterium Ruminococcus gauvreauii uncultured Lachnospiraceae bacterium Lachnospira eligens [Eubacterium] siraeum Eubacterium ruminantium +bsdb:1235/1/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Escherichia/Shigella sp. Eubacterium ruminantium Lachnospira eligens Ruminococcus gauvreauii [Eubacterium] siraeum uncultured Coriobacteriaceae bacterium uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium bsdb:1235/1/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA [Ruminococcus] torques uncultured Lachnospiraceae bacterium -bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA uncultured Oscillospiraceae bacterium uncultured Coriobacteriales bacterium Eubacterium coprostanoligenes +bsdb:1235/2/1_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA uncultured Coriobacteriales bacterium uncultured Oscillospiraceae bacterium bsdb:1235/2/2_Response-to-drug:Loxapine-Succinate-Low-Concentration(LOX-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Entacapone-Concentration(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA rumen bacterium NK4A214 -bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA Eubacterium coprostanoligenes uncultured Oscillospiraceae bacterium +bsdb:1235/3/1_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_UP NA uncultured Oscillospiraceae bacterium bsdb:1235/3/2_Response-to-drug:Entacapone-Low-Concentration(ENT-Low)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-High-(LOX-High),-Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-High(ENT-High)--after-24hours-of-incubation_DOWN NA uncultured Oscillospiraceae bacterium -bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA Eubacterium coprostanoligenes uncultured Coriobacteriales bacterium uncultured Oscillospiraceae bacterium [Ruminococcus] torques +bsdb:1235/4/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_UP NA [Ruminococcus] torques uncultured Coriobacteriales bacterium uncultured Oscillospiraceae bacterium bsdb:1235/4/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-24-hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low),-Entacapone-High(ENT-High)-and-Entacapone-Low(ENT-Low)--after-24hours-of-incubation_DOWN NA uncultured Oscillospiraceae bacterium -bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Escherichia/Shigella sp. +bsdb:1235/7/1_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_UP NA Streptococcus sp. +bsdb:1235/7/2_Response-to-drug:Loxapine-Succinate-High-Concentration(LOX-High)-after-6hrs-of-incubation_vs_Loxapine-Succinate-Low(LOX-Low)-and-Entacapone-Low(ENT-Low)-after-6hours-of-incubation_DOWN NA Clostridium sp. bsdb:1235/8/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA uncultured Christensenellaceae bacterium uncultured Lachnospiraceae bacterium [Clostridium] innocuum rumen bacterium NK4A214 bsdb:1235/8/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-1_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium bsdb:1235/9/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lachnospira eligens Escherichia/Shigella sp. -bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium [Ruminococcus] torques +bsdb:1235/9/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-2_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA [Ruminococcus] torques uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium Enterococcaceae bacterium RF39 bsdb:1235/10/1_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_UP NA Lachnospira eligens Escherichia/Shigella sp. bsdb:1235/10/2_Response-to-drug:Entacapone-High-Concentration(ENT-High)-after-24-hrs-of-incubation---Donor-3_vs_No-drug---Dimethyl-sulfoxide-only-(DMSO-only)_DOWN NA [Ruminococcus] torques uncultured Lachnospiraceae bacterium uncultured Oscillospiraceae bacterium bsdb:1237/1/1_Response-to-transplant:Cigarette-Smoke-exposed-FMT-mice-(CS-exposed-12-weeks)_vs_Air-exposed-FMT-mice---12-weeks_DOWN NA Kineothrix sp. Muricomes sp. Lachnospiraceae bacterium 14-2 diff --git a/file_size.csv b/file_size.csv index e9ad805d7..6014fd4e3 100644 --- a/file_size.csv +++ b/file_size.csv @@ -2574,3 +2574,4 @@ "2025-01-16_03:01_UTC" "4898" "5738" "4898" "5738" "4898" "5738" "6680" "6680" "6680" "3017" "3017" "3017" "3017" "3017" "3017" "4513" "7777" "7391" "1368" "2025-01-16_03:58_UTC" "4898" "5738" "4898" "5738" "4898" "5738" "6680" "6680" "6680" "3017" "3017" "3017" "3017" "3017" "3017" "4513" "7777" "7391" "1368" "2025-01-16_04:58_UTC" "4898" "5738" "4898" "5738" "4898" "5738" "6680" "6680" "6680" "3017" "3017" "3017" "3017" "3017" "3017" "4513" "7777" "7391" "1368" +"2025-01-16_05:58_UTC" "4897" "5737" "4897" "5737" "4897" "5737" "6680" "6680" "6680" "3018" "3018" "3018" "3018" "3018" "3018" "4513" "7777" "7391" "1368" diff --git a/full_dump.csv b/full_dump.csv index ffdbcf4b8..b3fafa103 100644 --- a/full_dump.csv +++ b/full_dump.csv @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-15_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-16_05:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org BSDB ID,Study,Study design,PMID,DOI,URL,Authors list,Title,Journal,Year,Keywords,Experiment,Location of subjects,Host species,Body site,UBERON ID,Condition,EFO ID,Group 0 name,Group 1 name,Group 1 definition,Group 0 sample size,Group 1 sample size,Antibiotics exclusion,Sequencing type,16S variable region,Sequencing platform,Statistical test,Significance threshold,MHT correction,LDA Score above,Matched on,Confounders controlled for,Pielou,Shannon,Chao1,Simpson,Inverse Simpson,Richness,Signature page name,Source,Curated date,Curator,Revision editor,Description,Abundance in Group 1,MetaPhlAn taxon names,NCBI Taxonomy IDs,State,Reviewer bsdb:1/1/1,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,144,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 1,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",increased,"k__Bacteria|p__Bacillota|c__Bacilli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Peptoniphilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Phascolarctobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Alcaligenaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae",2|1239|91061;2|1224|1236;2|201174|1760|2037|2049|1654;2|201174|1760|85007|1653|1716;2|1239|91061|186826|1300|1301;2|1239|1737404|1737405|1570339|162289;2|1239|186801|3085636|186803|189330;2|1239|909932|1843488|909930|33024;2|1224|28216|80840|995019|40544;2|201174|1760|2037;2|201174|1760|2037|2049;2|1224|28216|80840|506;2|1239|91061|186826;2|1239|91061|186826|1300;2|1239|909932|1843489|31977;2|1224|1236|91347;2|201174|1760|85007|1653;2|1239|91061|186826|33958|2759736|57037;2|1239|91061|1385|186817|1386;2|1239|91061|1385|186817,Complete,Fatima bsdb:1/1/2,Study 1,case-control,28038683,10.1186/s40168-016-0218-6,NA,"Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB , Ahn J",The gut microbiota in conventional and serrated precursors of colorectal cancer,Microbiome,2016,"Adenoma, Cancer, Colorectal, Microbiome, Microbiota, Polyp, Serrated",Experiment 1,United States of America,Homo sapiens,Feces,UBERON:0001988,Colorectal adenoma,EFO:0005406,controls,conventional adenoma cases,"conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.",323,144,NYU included who had not been on long-term antibiotic treatment,16S,4,Illumina,DESeq2,0.1,TRUE,NA,NA,"age,body mass index,sex",NA,decreased,NA,NA,NA,decreased,Signature 2,Table 2 + Supplemental Table S5 + S3+ S4,10 January 2021,Levi Waldron,WikiWorks,"Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level",decreased,"k__Bacteria|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Coprobacillus,k__Bacteria|p__Cyanobacteriota",2|1239|526524|526525|2810280|100883;2|1117,Complete,Shaimaa Elsafoury @@ -7300,7 +7300,7 @@ bsdb:1225/14/2,Study 1225,"cross-sectional observational, not case-control",3896 bsdb:1225/15/1,Study 1225,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL , Christakis NA","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 15,Honduras,Homo sapiens,Feces,UBERON:0001988,Water,CHEBI:15377,Subjects from the least well-off households based on water sources,Subjects from wealthier households based on water sources,"Subjects from wealthier households based on water sources refers to those with water sources such as: dug well, spring, tube well",NA,1610,NA,WMS,NA,Illumina,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 1,Table S1,19 November 2024,NA,NA,Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on water sources.,increased,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Catenibacterium|s__Catenibacterium sp. AM22-15,2|1783272|1239|526524|526525|2810280|135858|2292991,Complete,NA bsdb:1225/15/2,Study 1225,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL , Christakis NA","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 15,Honduras,Homo sapiens,Feces,UBERON:0001988,Water,CHEBI:15377,Subjects from the least well-off households based on water sources,Subjects from wealthier households based on water sources,"Subjects from wealthier households based on water sources refers to those with water sources such as: dug well, spring, tube well",NA,1610,NA,WMS,NA,Illumina,Mixed-Effects Regression,0.05,TRUE,NA,NA,"body mass index,sex",NA,decreased,NA,NA,NA,NA,Signature 2,Table S1,19 November 2024,NA,NA,Differential abundant taxa between Subjects from the least well-off households and Subjects from the wealthier households based on village sources.,decreased,NA,NA,Complete,NA bsdb:1225/16/1,Study 1225,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL , Christakis NA","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 16,Honduras,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Phenotypes without strain-phylogenetic information,Phenotypes with strain-phylogenetic information,"Phenotypes with strain-phylogenetic information refers to samples having strain-phylogenetic information, which were constructed by StrainPhlAn for each species, resulting in a tree comprising of individuals based on the genetic makeup of the species in their respective guts",NA,NA,NA,WMS,NA,Illumina,Mixed-Effects Regression,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 1,Table S9,19 November 2024,NA,NA,Differential abundant taxa between phenotypes with strain effect and phenotypes without strain effect.,increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus petauri,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus eutactus,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Parolsenella|s__Parolsenella massiliensis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium adolescentis,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides stercoris,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella|s__Paraprevotella clara,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus parasanguinis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter|s__Fusicatenibacter saccharivorans,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotellamassilia|s__Prevotellamassilia timonensis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AM49-4BH,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium sp. AM28-29,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|s__Clostridiaceae bacterium OM08-6BH,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia|s__Roseburia sp. AM59-24XD,k__Bacteria|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio piger,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia wexlerae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium fessum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lacrimispora|s__Lacrimispora amygdalina,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parainfluenzae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus catus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter|s__Agathobacter rectalis",2|1783272|1239|91061|186826|1300|1357|1940789;2|976|200643|171549|815|816|817;2|1783272|1239|186801|3085636|186803|33042|33043;2|1783272|201174|84998|84999|1643824|2082587|1871022;2|976|200643|171549|171552|838|1602169;2|1783272|201174|1760|85004|31953|1678|1680;2|976|200643|171549|815|816|46506;2|1783272|201174|84998|1643822|1643826|84108|572010;2|976|200643|171549|171552|2974251|2518605;2|1783272|1239|526524|526525|2810280|2678885|1982626;2|1783272|1239|186801|3085636|186803|28050|39485;2|976|200643|171549|171552|577309|454154;2|1783272|1239|91061|186826|1300|1301|1318;2|1783272|1239|186801|3085636|186803|1407607|1150298;2|976|200643|171549|171552|1926672|1852370;2|1783272|1239|186801|186802|31979|1485|2293035;2|1783272|1239|186801|186802|186806|1730|2292349;2|1783272|1239|186801|186802|31979|2292274;2|976|200643|171549|815|909656|821;2|1783272|1239|186801|186802|2527773|2500537;2|1783272|1239|186801|3085636|186803|841|2293138;2|200940|3031449|213115|194924|872|901;2|1783272|1239|186801|3085636|186803|572511|418240;2|1783272|1239|186801|186802|31979|1485|2126740;2|1783272|1239|186801|3085636|186803|2719231|253257;2|3379134|1224|1236|135625|712|724|729;2|1783272|1239|186801|3085636|186803|33042|116085;2|1783272|1239|186801|3082720|186804|1501226|1776391;2|1783272|1239|186801|3085636|186803|1766253|39491,Complete,NA -bsdb:1225/16/2,Study 1225,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL , Christakis NA","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 16,Honduras,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Phenotypes without strain-phylogenetic information,Phenotypes with strain-phylogenetic information,"Phenotypes with strain-phylogenetic information refers to samples having strain-phylogenetic information, which were constructed by StrainPhlAn for each species, resulting in a tree comprising of individuals based on the genetic makeup of the species in their respective guts",NA,NA,NA,WMS,NA,Illumina,Mixed-Effects Regression,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,19 November 2024,NA,NA,Differential abundant taxa between phenotypes with strain effect and phenotypes without strain effect.,decreased,"k__Bacteria|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens",2|74201|203494|48461|1647988|239934|239935;2|976|200643|171549|171550|239759|1288121;2|1783272|1239|186801|186802|2527773|2500537;2|1783272|1239|186801|186802|31979|1485|2292206;2|1783272|1239|186801|186802|31979|1485|2293015;2|1783272|1239|526524|526525|2810280|2678885|1982626;2|256845|1313211|2053569;2157|3366610|28890|183925|2158|2159|2172|2173;2|1783272|1239|186801|186802|216572|459786|1519439;2|976|200643|171549|171552|838|1602169;2|976|200643|171549|171552|2974251|2518605;2|1783272|201174|84998|1643822|1643826|84108|572010,Complete,NA +bsdb:1225/16/2,Study 1225,"cross-sectional observational, not case-control",38968070,10.1016/j.celrep.2024.114442,NA,"Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL , Christakis NA","Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages",Cell reports,2024,"CP: Microbiology, economic factors, gut microbiome species, gut microbiome strains, non-western LMIC cohort, polymorphic sites, population-wide microbiome associations, social networks, uncharacterized taxa",Experiment 16,Honduras,Homo sapiens,Feces,UBERON:0001988,Lifestyle measurement,EFO:0010724,Phenotypes without strain-phylogenetic information,Phenotypes with strain-phylogenetic information,"Phenotypes with strain-phylogenetic information refers to samples having strain-phylogenetic information, which were constructed by StrainPhlAn for each species, resulting in a tree comprising of individuals based on the genetic makeup of the species in their respective guts",NA,NA,NA,WMS,NA,Illumina,Mixed-Effects Regression,0.05,TRUE,NA,NA,body mass index,NA,NA,NA,NA,NA,NA,Signature 2,Table S9,19 November 2024,KateRasheed,KateRasheed,Differential abundant taxa between phenotypes with strain effect and phenotypes without strain effect.,decreased,"k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Candidatus Cibiobacter|s__Candidatus Cibiobacter qucibialis,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF27-2AA,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp. AF36-4,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Faecalibacillus|s__Faecalibacillus intestinalis,k__Bacteria|k__Pseudomonadati|p__Lentisphaerota|c__Lentisphaeria|s__Lentisphaeria bacterium,k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter smithii,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Mitsuokella|s__Mitsuokella multacida,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter sp. ER4,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella pectinovora,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Segatella|s__Segatella hominis,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia|s__Slackia isoflavoniconvertens",2|3379134|74201|203494|48461|1647988|239934|239935;2|3379134|976|200643|171549|171550|239759|1288121;2|1783272|1239|186801|186802|2527773|2500537;2|1783272|1239|186801|186802|31979|1485|2292206;2|1783272|1239|186801|186802|31979|1485|2293015;2|1783272|1239|526524|526525|2810280|2678885|1982626;2|3379134|256845|1313211|2053569;2157|3366610|28890|183925|2158|2159|2172|2173;2|1783272|1239|909932|909929|1843491|52225|52226;2|1783272|1239|186801|186802|216572|459786|1519439;2|3379134|976|200643|171549|171552|838|1602169;2|3379134|976|200643|171549|171552|2974251|2518605;2|1783272|201174|84998|1643822|1643826|84108|572010,Complete,NA bsdb:1226/1/1,Study 1226,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S, Vera-Ponce de León A, Kodama M, Hoetzinger M, Clausen CG, Pless L, Verissimo ARA, Stengel B, Calabuig V, Kvingedal R, Skugor S, Westereng B, Harvey TN, Nordborg A, Bertilsson S, Limborg MT, Mørkøre T, Sandve SR, Pope PB, Hvidsten TR , La Rosa SL",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 1,Norway,Salmo salar,Hindgut,UBERON:0001046,Response to diet,EFO:0010757,0.2% CTR Diet T2,0.2% MC2 Diet T2,"Salmon fed a standard commercial diet supplemented with 0.2% MC2 (a 0.2% w/w α-mannan supplement produced by Cargill) at 10 weeks (T2, smolt stage) after the experiment started.",30,30,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 1G,18 November 2024,YokoC,YokoC,"Significant differential abundances (Wilcoxon test) for bacterial genera in salmons fed a 0.2% MC2 diet or a CTR (control) diet at 10 weeks (T2, smolt stage) after the experiment began.",increased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum",2|3379134|1224|28216|80840|119060|106589;2|3379134|1224|28216|80840|75682|963;2|3379134|1224|28211|204441|2829815|1543705,Complete,Svetlana up bsdb:1226/2/1,Study 1226,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S, Vera-Ponce de León A, Kodama M, Hoetzinger M, Clausen CG, Pless L, Verissimo ARA, Stengel B, Calabuig V, Kvingedal R, Skugor S, Westereng B, Harvey TN, Nordborg A, Bertilsson S, Limborg MT, Mørkøre T, Sandve SR, Pope PB, Hvidsten TR , La Rosa SL",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 2,Norway,Salmo salar,Hindgut,UBERON:0001046,Response to diet,EFO:0010757,0.2% CTR Diet T2,0.2% MN3 Diet T2,"Salmon fed with a standard commercial diet supplemented with 0.2% MN3 (0.2% w/w acetylated β-galactoglucomannan) at 10 weeks (T2, smolt stage) after the experiment started.",30,30,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,Fig. 1G,18 November 2024,YokoC,YokoC,"Significant differential abundances (Wilcoxon test) for bacterial genera in salmons fed a 0.2% MN3 diet or a CTR (control) diet at 10 weeks (T2, smolt stage) after the experiment began.",increased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Herbaspirillum,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Rhodospirillales|f__Azospirillaceae|g__Nitrospirillum",2|3379134|1224|28216|80840|119060|106589;2|3379134|1224|28216|80840|75682|963;2|3379134|1224|28211|204441|2829815|1543705,Complete,Svetlana up bsdb:1226/3/1,Study 1226,laboratory experiment,39455736,10.1038/s42003-024-07087-4,NA,"Gupta S, Vera-Ponce de León A, Kodama M, Hoetzinger M, Clausen CG, Pless L, Verissimo ARA, Stengel B, Calabuig V, Kvingedal R, Skugor S, Westereng B, Harvey TN, Nordborg A, Bertilsson S, Limborg MT, Mørkøre T, Sandve SR, Pope PB, Hvidsten TR , La Rosa SL",The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production,Communications biology,2024,NA,Experiment 3,Norway,Salmo salar,Actinopterygian pyloric caecum,UBERON:4300174,Response to diet,EFO:0010757,4% CTR Diet Pyloric caecum,4% MN3 Pyloric caecum,Salmon fed with a standard commercial diet supplemented with 4% MN3 ( 4% w/w acetylated β-galactoglucomannan) for 4 weeks.,18,18,NA,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Fig. 2F,18 November 2024,YokoC,"YokoC,Aleru Divine",Significant differential abundances (Wilcoxon test) for bacterial genera in samples collected from the pyloric caecum of salmons fed a 4% MN3 diet or a CTR diet.,increased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|3379134|1224|28216|80840|80864;2|3379134|1224|1236|72274|135621|286,Complete,Svetlana up @@ -7411,25 +7411,25 @@ bsdb:1233/1/1,Study 1233,time series / longitudinal observational,30007242,10.10 bsdb:1233/1/2,Study 1233,time series / longitudinal observational,30007242,10.1016/j.eplepsyres.2018.06.015,NA,"Zhang Y, Zhou S, Zhou Y, Yu L, Zhang L , Wang Y",Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet,Epilepsy research,2018,"Children, Gut microbiota, Ketogenic diet, Refractory epilepsy",Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Ketogenic diet,EFO:0009371,pre-treatment group,treatment group,Group treated for 6 months with ketogenic diet therapy,20,20,two weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,unchanged,unchanged,unchanged,NA,NA,Signature 2,Figure 2,20 November 2024,Kavyaayala,Kavyaayala,Comparing difference in fecal microbiome of KD treated children after treatment implementation vs before treatment,decreased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacteria|k__Bacillati|p__Actinomycetota,k__Bacteria|k__Bacillati|p__Bacillota,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Leucobacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas",2|3379134|1224|1236|2887326|468|469;2|1783272|201174|1760|2037;2|1783272|201174|1760;2|1783272|201174;2|1783272|1239;2|3379134|1224|28216|80840|119060;2|1783272|1239|186801;2|976|200643|171549|2005519|1348911;2|1783272|1239|186801|186802;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|3085636|186803;2|1783272|201174|1760|85006|85023|55968;2|1783272|201174|1760|85006|85023;2|3379134|1224|1236|2887326|468;2|1783272|1239|186801|186802|216572;2|3379134|1224|1236|72274|135621;2|3379134|1224|1236|72274;2|3379134|1224|1236|72274|135621|286,Complete,NA bsdb:1233/2/1,Study 1233,time series / longitudinal observational,30007242,10.1016/j.eplepsyres.2018.06.015,NA,"Zhang Y, Zhou S, Zhou Y, Yu L, Zhang L , Wang Y",Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet,Epilepsy research,2018,"Children, Gut microbiota, Ketogenic diet, Refractory epilepsy",Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Response to ketogenic diet,EFO:0009372,responders,non-responders,patients who had less than 50% of seizure frequency reduction,10,10,two weeks,16S,34,Illumina,LEfSe,0.05,FALSE,2,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 3,25 November 2024,Kavyaayala,Kavyaayala,Comparing difference in fecal microbiome of non-responders to responders,increased,"k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes,k__Bacteria|k__Bacillati|p__Actinomycetota,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|1783272|201174|1760;2|1783272|201174;2|976|200643|171549|171550|239759;2|1783272|1239|186801|186802|216572|244127;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801;2|1783272|201174|84998|84999|84107;2|1783272|201174|84998|84999;2|1783272|1239|186801|3085636|186803|189330;2|1783272|201174|84998|1643822|1643826|84111;2|1783272|1239|186801|186802;2|1783272|1239|186801|3085636|186803|1407607;2|1783272|201174|84998|1643822|1643826|644652;2|29547|3031852|213849|72293|209;2|29547|3031852|213849|72293;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572|459786;2|1783272|1239|186801|186802|216572;2|976|200643|171549|171550;2|1783272|1239|186801|186802|216572|1263;2|1783272|1239|91061|186826|1300;2|1783272|1239|91061|186826|1300|1301,Complete,NA bsdb:1234/1/2,Study 1234,laboratory experiment,35310158,10.7717/peerj.13095,NA,"Bensch HM, Tolf C, Waldenström J, Lundin D , Zöttl M",Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples,PeerJ,2022,"16S, Amplicon, DNA metabarcoding, Damaraland mole-rat, Fecal samples, Freeze-drying, Fukomys damarensis, Microbiome",Experiment 1,South Africa,Fukomys damarensis,Feces,UBERON:0001988,Freeze dried specimen,EFO:0005121,Frozen samples,Freeze dried samples.,Freeze dried samples are samples preservation treatment stored and transported at ambient temperature until DNA extraction.,20,20,NA,16S,34,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,unchanged,Signature 2,"Figure 4, Table S1",21 November 2024,Tosin,Tosin,Log-transformed relative abundances of families with > 1% mean relative abundance between Frozen and Freeze-dried sample preservation treatments.,decreased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|1783272|1239|186801|3082768|990719;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572,Complete,NA -bsdb:1235/1/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 1,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 24hours of incubation",Entacapone High Concentration(ENT-High) after 24 hrs of incubation,"Entacapone High Concentration(ENT-High) after 24hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1783272|1239|186801|186802|186806|1730|290054;2|1783272|1239|186801|186802|1980681;2|1783272|1239|91061|186826;2|3379134|1224|1236|91347|543|1940338;2|1783272|201174|84998|84999|84107|331632;2|1783272|1239|186801|186802|216572|707003;2|1783272|201174|84998|1643822|1643826;2|1783272|1239|186801|186802|216572|1263|438033;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|3085636|186803|28050|39485;2|1783272|1239|186801|186802|216572|1263;2|1783272|1239|186801|3085636|186803|189330;2|1783272|1239|186801|3085636|186803|28050;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|526524|526525|128827|1573535;2|1783272|1239|186801|186802|216572|39492;2|1783272|1239|186801|3085636|186803|33042;2|1783272|1239|186801|186802|216572|292632;2|1783272|1239|186801|186802|186806|1730|42322;2|1783272|1239|186801|3085636|186803|841;2|1783272|1239|186801|186802|3085642|580596;2|1783272|1239|186801|3085636|186803,Complete,NA -bsdb:1235/1/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 1,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 24hours of incubation",Entacapone High Concentration(ENT-High) after 24 hrs of incubation,"Entacapone High Concentration(ENT-High) after 24hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|p__Lentisphaerota,k__Bacteria|k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae",2|1783272|1239|186801|3085636|186803|1766253;2|976|200643|171549|171550|239759;2|1783272|1239|186801|3085636|186803|207244;2|1783272|201174|84998|84999|84107|102106;2|1783272|1239|186801|3085636|186803|33042;2|1783272|1239|186801|3085636|186803|1407607;2157|3366610|28890|183925|2158|2159|2172;2|976|200643|171549|2005525|375288;2|1783272|201174|84998|84999|84107|1473205;2|3379134|1224|28216|80840|995019|40544;2|1783272|1239|186801|3085636|186803|2316020|33039;2|256845;2|1783272|1798710|1906119;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|526524|526525|2810280|3025755;2|976|200643|171549|815|816;2|1783272|201174|1760|85004|31953|1678;2|1783272|201174|84998|1643822|1643826|84111;2|1783272|1239|186801|186802|31979|1485;2|1783272|1239|186801|3085636|186803|572511;2|976|200643|171549|2005519|1348911;2|1783272|1239|526524|526525|128827|1470349;2|1783272|1239|186801|186802|216572|216851;2|1783272|201174|84998|1643822|1643826|644652;2|976|200643|171549|2005473,Complete,NA -bsdb:1235/2/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 2,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Entacapone Concentration(ENT-High) and Entacapone Low(ENT-Low) after 24hours of incubation",Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation.,9,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes",2|1783272|201174|84998|1643822|1643826;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|186802|216572|707003;2|1783272|201174|84998|84999|349920;2|1783272|1239|91061|186826;2|976|117743|200644;2|1783272|1239|186801|186802|186806|1730|290054,Complete,NA -bsdb:1235/2/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 2,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Entacapone Concentration(ENT-High) and Entacapone Low(ENT-Low) after 24hours of incubation",Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation.,9,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|s__rumen bacterium NK4A214",2|976|200643|171549|815|816;2|1783272|201174|1760|2037|2049|1654;2|1783272|1239|186801|3085636|186803;2|1783272|1239|526524|526525|128827;2|877428,Complete,NA -bsdb:1235/3/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 3,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone High(ENT-High) after 24hours of incubation",Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation,Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,9,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales",2|1783272|1239|186801|186802|1980681;2|1783272|201174|84998|1643822|1643826;2|1783272|1239|186801|186802|186806|1730|290054;2|1783272|1239|186801|186802|216572|707003;2|976|117743|200644,Complete,NA -bsdb:1235/3/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 3,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone High(ENT-High) after 24hours of incubation",Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation,Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,9,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1783272|1239|186801|186802|216572|292632;2|1783272|1239|186801|186802|216572|707003,Complete,NA -bsdb:1235/4/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 4,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate Low(LOX-Low), Entacapone High(ENT-High) and Entacapone Low(ENT-Low) after 24hours of incubation",Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation,"Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium coprostanoligenes,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|976|200643|171549|171550|239759;2|1783272|1239|91061|186826;2|1783272|201174|84998|1643822|1643826;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|186802|186806|1730|290054;2|1783272|201174|84998|84999|349920;2|1783272|1239|186801|3085636|186803|207244;2|1783272|1239|186801|186802|216572|707003;2|1783272|1239|186801|3085636|186803|2316020|33039;2|1783272|1239|186801|3085636|186803|572511,Complete,NA -bsdb:1235/4/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 4,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate Low(LOX-Low), Entacapone High(ENT-High) and Entacapone Low(ENT-Low) after 24hours of incubation",Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation,"Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|815|816;2|1783272|201174|1760|85004|31953|1678;2|1783272|1798710|1906119;2|1783272|1239|186801|186802|31979|1485;2|1783272|1239|186801|186802|216572|946234;2|976|200643|171549|171552|577309;2|1783272|1239|526524|526525|2810280|3025755;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572|707003,Complete,NA -bsdb:1235/5/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 5,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1783272|1239|91061|186826|1300|1301,Complete,NA -bsdb:1235/5/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 5,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA -bsdb:1235/6/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 6,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Loxapine Succinate Low(LOX-Low) after 6hours of incubation,Entacapone Low Concentration(ENT-Low) after 6hrs of incubation,Entacapone Low Concentration(ENT-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1783272|1239|91061|186826|1300|1301,Complete,NA -bsdb:1235/7/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 7,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,6,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1783272|1239|91061|186826|1300|1301,Complete,NA -bsdb:1235/7/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 7,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,6,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",decreased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium",2|3379134|1224|1236|91347|543|1940338;2|1783272|1239|186801|186802|31979|1485,Complete,NA -bsdb:1235/8/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 8,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 1,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 1 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,NA,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 1 after 24hrs of incubation.,increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__uncultured Christensenellaceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|s__rumen bacterium NK4A214,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1783272|1239|186801|186802|216572|459786;2|1783272|1239|186801|3082768|990719|1229255;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|526524|526525|128827|1522;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|3085636|186803|841;2|877428;2|1783272|201174|1760|85004|31953|1678,Complete,NA -bsdb:1235/8/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 8,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 1,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 1 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,NA,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 1 after 24hrs of incubation.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|3085636|186803|189330;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|186802|216572|946234;2|1783272|1239|186801|3085636|186803|1407607;2|1783272|1239|526524|526525|128827|1573535;2|1783272|1239|186801|3085636|186803|1506553;2|1783272|1239|91061|186826|33958|2759736;2|1783272|1239|186801|3085636|186803|248744;2|1783272|1239|526524|526525|2810280|3025755;2|976|117743|200644;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|186802|216572|707003,Complete,NA -bsdb:1235/9/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 9,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 2,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 2 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,NA,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 2 after 24hrs of incubation.,increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",2|1783272|1239|91061|186826|33958|2759736;2|1783272|201174|1760|2037|2049|1654;2|1783272|1239|186801|186802|216572;2|1783272|1239|186801|186802|216572;2|1783272|201174|84998|1643822|1643826|1926677;2|1783272|201174|84998|84999|84107|102106;2|1783272|1239|186801|3082720|3030910|86331;2|1783272|1239|526524|526525|128827|1573535;2|1783272|1239|91061|186826|186828|117563;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|186802|3085642|580596;2|1783272|1239|186801|3085636|186803|248744;2|976|200643|171549|2005519|397864;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|909932|1843489|31977|29465;2|1783272|1239|186801|3085636|186803|28050|39485;2|1783272|1239|186801|3085636|186803|572511;2|3379134|1224|1236|91347|543|1940338;2|3379134|1224|1236|91347|543|544;2|3379134|1224|1236|91347|543;2|1783272|201174|1760|85004|31953|1678;2|1783272|1239|186801|3085636|186803|28050;2|1783272|1239|186801|3082720|186804|1505652;2|1783272|1239|186801|3085636|186803;2|1783272|1239|909932|1843489|31977|906;2|1783272|1239|186801|3085636|186803|1766253;2|1783272|1239|909932|1843488|909930|904,Complete,NA -bsdb:1235/9/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 9,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 2,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 2 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,NA,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 2 after 24hrs of incubation.,decreased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques",2|1783272|1239|186801|3085636|186803|33042;2|976|200643|171549|2005525|375288;2|3379134|1224|28216|80840|995019|40544;2|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|3085636|186803|207244;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|3085636|186803|1407607;2|1783272|1239|526524|526525|2810280|3025755;2|976|200643|171549|171550|239759;2|976|200643|171549|1853231|574697;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|186802|216572|459786;2|1783272|1239|186801|186802|216572|707003;2|1783272|201174|84998|1643822|1643826|84108;2|1783272|1239|186801|3085636|186803|2316020|33039,Complete,NA -bsdb:1235/10/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 10,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 3,"Entacapone High Concentration(ENT-High) after 24 hrs of incubation, refers to the drug concentration given to donor 3 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",NA,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 3 after 24hrs of incubation.,increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1783272|1239|91061|186826|33958|2759736;2|1783272|1239|186801|186802|216572;2|1783272|1239|186801|186802|216572;2|1783272|201174|1760|2037|2049|1654;2|1783272|201174|84998|1643822|1643826|1926677;2|1783272|201174|84998|84999|84107|102106;2|1783272|1239|186801|3082720|3030910|86331;2|1783272|1239|526524|526525|128827|1573535;2|1783272|1239|91061|186826|186828|117563;2|1783272|1239|186801|3085636|186803|248744;2|1783272|1239|186801|186802|3085642|580596;2|976|200643|171549|2005519|397864;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|909932|1843489|31977|29465;2|1783272|1239|186801|3085636|186803|28050|39485;2|1783272|1239|186801|3085636|186803|572511;2|3379134|1224|1236|91347|543|1940338;2|3379134|1224|1236|91347|543;2|3379134|1224|1236|91347|543|544;2|1783272|201174|1760|85004|31953|1678;2|1783272|1239|186801|3085636|186803|28050;2|1783272|1239|186801|3082720|186804|1505652;2|1783272|1239|909932|1843489|31977|906;2|1783272|1239|909932|1843488|909930|904;2|1783272|1239|186801|3085636|186803|1766253;2|1783272|1239|186801|3085636|186803,Complete,NA -bsdb:1235/10/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 10,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 3,"Entacapone High Concentration(ENT-High) after 24 hrs of incubation, refers to the drug concentration given to donor 3 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",NA,3,3 months,16S,NA,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 3 after 24hrs of incubation.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|171550|239759;2|1783272|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511;2|976|200643|171549|1853231|574697;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|3085636|186803|33042;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|3085636|186803|1407607;2|1783272|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|3379134|1224|28216|80840|995019|40544;2|1783272|1239|526524|526525|2810280|3025755;2|1783272|1239|186801|3085636|186803|2316020|33039;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|186802|216572|707003,Complete,NA +bsdb:1235/1/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 1,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 24hours of incubation",Entacapone High Concentration(ENT-High) after 24 hrs of incubation,"Entacapone High Concentration(ENT-High) after 24hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium ruminantium,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus|s__Ruminococcus gauvreauii,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__[Eubacterium] siraeum,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|s__uncultured Coriobacteriaceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|186802|3085642|580596;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|3085636|186803|33042;2|1783272|1239|186801|3085636|186803|189330;2|3379134|1224|1236|91347|543|1940338;2|1783272|1239|186801|186802|186806|1730|42322;2|1783272|1239|526524|526525|128827|1573535;2|1783272|1239|186801|3085636|186803|28050;2|1783272|1239|186801|3085636|186803|28050|39485;2|1783272|1239|186801|3085636|186803|841;2|1783272|1239|186801|186802|216572|1263;2|1783272|1239|186801|186802|216572|1263|438033;2|1783272|1239|186801|186802|216572|292632;2|1783272|1239|186801|186802|216572|39492;2|1783272|201174|84998|1643822|1643826;2|1783272|1239|186801|3085636|186803;2|1783272|1239|91061|186826;2|1783272|201174|84998|84999|84107|331632;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|186802|216572|707003,Complete,NA +bsdb:1235/1/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 1,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 24hours of incubation",Entacapone High Concentration(ENT-High) after 24 hrs of incubation,"Entacapone High Concentration(ENT-High) after 24hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Candidatus Stoquefichus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Coprobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter,k__Archaea|k__Methanobacteriati|p__Methanobacteriota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|k__Pseudomonadati|p__Lentisphaerota,k__Bacteria|k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium",2|1783272|1239|186801|3085636|186803|1766253;2|3379134|976|200643|171549|171550|239759;2|1783272|1239|186801|3085636|186803|207244;2|3379134|976|200643|171549|815|816;2|1783272|201174|1760|85004|31953|1678;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|526524|526525|128827|1470349;2|1783272|1239|186801|186802|31979|1485;2|1783272|201174|84998|84999|84107|102106;2|3379134|976|200643|171549|2005519|1348911;2|1783272|1239|186801|3085636|186803|33042;2|1783272|201174|84998|1643822|1643826|84111;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|3085636|186803|1407607;2|1783272|201174|84998|1643822|1643826|644652;2157|3366610|28890|183925|2158|2159|2172;2|3379134|976|200643|171549|2005525|375288;2|1783272|201174|84998|84999|84107|1473205;2|3379134|1224|28216|80840|995019|40544;2|1783272|1239|526524|526525|2810280|3025755;2|1783272|1239|186801|3085636|186803|2316020|33039;2|3379134|256845;2|1783272|1798710|1906119;2|1783272|1239|186801|3085636|186803;2|3379134|976|200643|171549|2005473;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|3085636|186803|1506553,Complete,NA +bsdb:1235/2/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 2,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Entacapone Concentration(ENT-High) and Entacapone Low(ENT-Low) after 24hours of incubation",Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation.,9,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1783272|1239|186801|186802|1980681;2|1783272|201174|84998|1643822|1643826;2|3379134|976|117743|200644;2|1783272|1239|91061|186826;2|1783272|201174|84998|84999|349920;2|1783272|1239|186801|186802|216572|707003,Complete,NA +bsdb:1235/2/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 2,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Entacapone Concentration(ENT-High) and Entacapone Low(ENT-Low) after 24hours of incubation",Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation.,9,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae,k__Bacteria|s__rumen bacterium NK4A214",2|976|200643|171549|815|816;2|1783272|201174|1760|2037|2049|1654;2|1783272|1239|186801|3085636|186803;2|1783272|1239|526524|526525|128827;2|877428,Complete,NA +bsdb:1235/3/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 3,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone High(ENT-High) after 24hours of incubation",Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation,Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,9,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1783272|1239|186801|186802|1980681;2|1783272|201174|84998|1643822|1643826;2|3379134|976|117743|200644;2|1783272|1239|186801|186802|216572|707003,Complete,NA +bsdb:1235/3/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 3,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate High (LOX-High), Loxapine Succinate Low(LOX-Low) and Entacapone High(ENT-High) after 24hours of incubation",Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation,Entacapone Low Concentration(ENT-Low) after 24 hrs of incubation refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,9,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,21 November 2024,NA,NA,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1783272|1239|186801|186802|216572|292632;2|1783272|1239|186801|186802|216572|707003,Complete,NA +bsdb:1235/4/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 4,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate Low(LOX-Low), Entacapone High(ENT-High) and Entacapone Low(ENT-Low) after 24hours of incubation",Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation,"Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,21 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",increased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|s__uncultured Coriobacteriales bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|3379134|976|200643|171549|171550|239759;2|1783272|1239|186801|3085636|186803|207244;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|3085636|186803|2316020|33039;2|1783272|201174|84998|1643822|1643826;2|1783272|1239|91061|186826;2|1783272|201174|84998|84999|349920;2|1783272|1239|186801|186802|216572|707003,Complete,NA +bsdb:1235/4/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 4,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,"Loxapine Succinate Low(LOX-Low), Entacapone High(ENT-High) and Entacapone Low(ENT-Low) after 24hours of incubation",Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation,"Loxapine Succinate High Concentration(LOX-High) after 24 hrs of incubation, refers to the drug concentration given to the six healthy adult individuals after twenty-four hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",9,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-High, ENT-Low, LOX-High and LOX-Low) after 24hrs of incubation.",decreased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Paraprevotella,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|k__Bacillati|p__Candidatus Melainabacteria|o__Candidatus Gastranaerophilales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|3379134|976|200643|171549|815|816;2|1783272|201174|1760|85004|31953|1678;2|1783272|1239|186801|186802|31979|1485;2|1783272|1239|186801|186802|216572|946234;2|3379134|976|200643|171549|171552|577309;2|1783272|1239|526524|526525|2810280|3025755;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572|707003;2|1783272|1798710|1906119;2|1783272|1239|186801|3085636|186803|1506553;2|1783272|1239|186801|186802|216572,Complete,NA +bsdb:1235/5/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 5,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1783272|1239|91061|186826|1300|1301,Complete,NA +bsdb:1235/5/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 5,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation,Loxapine Succinate Low Concentration(LOX-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",decreased,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,2|976|200643|171549|815|816,Complete,NA +bsdb:1235/6/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 6,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate High (LOX-High) and Loxapine Succinate Low(LOX-Low) after 6hours of incubation,Entacapone Low Concentration(ENT-Low) after 6hrs of incubation,Entacapone Low Concentration(ENT-Low) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. The low drug concentration was previously used in a screening aimed at determining drug effects on pure culture isolates.,6,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,2|1783272|1239|91061|186826|1300|1301,Complete,NA +bsdb:1235/7/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 7,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,6,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",increased,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus sp.,2|1783272|1239|91061|186826|1300|1301|1306,Complete,NA +bsdb:1235/7/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 7,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,Loxapine Succinate Low(LOX-Low) and Entacapone Low(ENT-Low) after 6hours of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation,Loxapine Succinate High Concentration(LOX-High) after 6hrs of incubation refers to the drug concentration given to the six healthy adult individuals after six hours of incubation. Loxapine succinate is a tricyclic antipsychotic medication primarily used in the treatment of schizophrenia. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,6,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Table 5,22 November 2024,KateRasheed,KateRasheed,"Differential abundance of taxa between the drug-amendment experiments(ENT-Low, LOX-High and LOX-Low) after 6hrs of incubation.",decreased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium sp.,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides",2|1783272|1239|186801|186802|31979|1485|1506;2|3379134|976|200643|171549|815|816,Complete,NA +bsdb:1235/8/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 8,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 1,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 1 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,3,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 1 after 24hrs of incubation.,increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Christensenellales|f__Christensenellaceae|s__uncultured Christensenellaceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|s__[Clostridium] innocuum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|s__rumen bacterium NK4A214,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium",2|1783272|1239|186801|186802|216572|459786;2|1783272|1239|186801|3082768|990719|1229255;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|526524|526525|128827|1522;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|3085636|186803|841;2|877428;2|1783272|201174|1760|85004|31953|1678,Complete,NA +bsdb:1235/8/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 8,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 1,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 1 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,3,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 1 after 24hrs of incubation.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Dorea,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoclostridium,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|3085636|186803|189330;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|186802|216572|946234;2|1783272|1239|186801|3085636|186803|1407607;2|1783272|1239|526524|526525|128827|1573535;2|1783272|1239|186801|3085636|186803|1506553;2|1783272|1239|91061|186826|33958|2759736;2|1783272|1239|186801|3085636|186803|248744;2|1783272|1239|526524|526525|2810280|3025755;2|976|117743|200644;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|186802|216572|707003,Complete,NA +bsdb:1235/9/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 9,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 2,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 2 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,3,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 2 after 24hrs of incubation.,increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus",2|1783272|1239|91061|186826|33958|2759736;2|1783272|201174|1760|2037|2049|1654;2|1783272|1239|186801|186802|216572;2|1783272|1239|186801|186802|216572;2|1783272|201174|84998|1643822|1643826|1926677;2|1783272|201174|84998|84999|84107|102106;2|1783272|1239|186801|3082720|3030910|86331;2|1783272|1239|526524|526525|128827|1573535;2|1783272|1239|91061|186826|186828|117563;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|186802|3085642|580596;2|1783272|1239|186801|3085636|186803|248744;2|976|200643|171549|2005519|397864;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|909932|1843489|31977|29465;2|1783272|1239|186801|3085636|186803|28050|39485;2|1783272|1239|186801|3085636|186803|572511;2|3379134|1224|1236|91347|543|1940338;2|3379134|1224|1236|91347|543|544;2|3379134|1224|1236|91347|543;2|1783272|201174|1760|85004|31953|1678;2|1783272|1239|186801|3085636|186803|28050;2|1783272|1239|186801|3082720|186804|1505652;2|1783272|1239|186801|3085636|186803;2|1783272|1239|909932|1843489|31977|906;2|1783272|1239|186801|3085636|186803|1766253;2|1783272|1239|909932|1843488|909930|904,Complete,NA +bsdb:1235/9/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 9,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 2,Entacapone High Concentration(ENT-High) after 24 hrs of incubation refers to the drug concentration given to donor 2 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.,3,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,KateRasheed,KateRasheed,Differential abundance of taxa between No drug and ENT-High in Donor 2 after 24hrs of incubation.,decreased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Slackia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|s__Enterococcaceae bacterium RF39",2|3379134|976|200643|171549|171550|239759;2|1783272|1239|186801|3085636|186803|207244;2|3379134|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511;2|3379134|976|200643|171549|1853231|574697;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|3085636|186803|33042;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|3085636|186803|1407607;2|1783272|1239|186801|186802|216572|459786;2|3379134|976|200643|171549|2005525|375288;2|1783272|201174|84998|1643822|1643826|84108;2|3379134|1224|28216|80840|995019|40544;2|1783272|1239|526524|526525|2810280|3025755;2|1783272|1239|186801|3085636|186803|2316020|33039;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|186802|216572|707003;2|1783272|1239|91061|186826|81852|423410,Complete,NA +bsdb:1235/10/1,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 10,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 3,"Entacapone High Concentration(ENT-High) after 24 hrs of incubation, refers to the drug concentration given to donor 3 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",3,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 1,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 3 after 24hrs of incubation.,increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Raoultibacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Anaerovoracaceae|g__Mogibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Holdemanella,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Marvinbryantia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Butyricicoccaceae|g__Butyricicoccus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Barnesiellaceae|g__Barnesiella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira|s__Lachnospira eligens,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|s__Escherichia/Shigella sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnospira,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Terrisporobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Acidaminococcales|f__Acidaminococcaceae|g__Acidaminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Agathobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae",2|1783272|1239|91061|186826|33958|2759736;2|1783272|1239|186801|186802|216572;2|1783272|1239|186801|186802|216572;2|1783272|201174|1760|2037|2049|1654;2|1783272|201174|84998|1643822|1643826|1926677;2|1783272|201174|84998|84999|84107|102106;2|1783272|1239|186801|3082720|3030910|86331;2|1783272|1239|526524|526525|128827|1573535;2|1783272|1239|91061|186826|186828|117563;2|1783272|1239|186801|3085636|186803|248744;2|1783272|1239|186801|186802|3085642|580596;2|976|200643|171549|2005519|397864;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|909932|1843489|31977|29465;2|1783272|1239|186801|3085636|186803|28050|39485;2|1783272|1239|186801|3085636|186803|572511;2|3379134|1224|1236|91347|543|1940338;2|3379134|1224|1236|91347|543;2|3379134|1224|1236|91347|543|544;2|1783272|201174|1760|85004|31953|1678;2|1783272|1239|186801|3085636|186803|28050;2|1783272|1239|186801|3082720|186804|1505652;2|1783272|1239|909932|1843489|31977|906;2|1783272|1239|909932|1843488|909930|904;2|1783272|1239|186801|3085636|186803|1766253;2|1783272|1239|186801|3085636|186803,Complete,NA +bsdb:1235/10/2,Study 1235,randomized controlled trial,39572788,10.1038/s41564-024-01853-0,NA,"Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvári D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Böttcher T, Cheng JX , Wagner M",The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration,Nature microbiology,2024,NA,Experiment 10,"Austria,United Kingdom",Homo sapiens,Feces,UBERON:0001988,Response to drug,GO:0009410,No drug - Dimethyl sulfoxide only (DMSO only),Entacapone High Concentration(ENT-High) after 24 hrs of incubation - Donor 3,"Entacapone High Concentration(ENT-High) after 24 hrs of incubation, refers to the drug concentration given to donor 3 after twenty-four hours of incubation. Entacapone is a catechol-O-methyltransferase (COMT) inhibitor that acts by preventing the degradation of levodopa. It is the main drug used in the treatment of Parkinson’s disease. High concentration was based on estimated colon concentration and was included to better reflect the exposure of gut microbes to drugs in the large intestine.",3,3,3 months,16S,4,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,decreased,decreased,Signature 2,Supplementary Table 6,22 November 2024,NA,NA,Differential abundance of taxa between No drug and ENT-High in Donor 3 after 24hrs of incubation.,decreased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Anaerostipes,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Odoribacteraceae|g__Butyricimonas,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|g__Colidextribacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Coprococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Fusicatenibacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Oscillibacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Coprobacillaceae|g__Thomasclavelia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Mediterraneibacter|s__[Ruminococcus] torques,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|976|200643|171549|171550|239759;2|1783272|1239|186801|3085636|186803|207244;2|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511;2|976|200643|171549|1853231|574697;2|1783272|1239|186801|186802|1980681;2|1783272|1239|186801|3085636|186803|33042;2|1783272|1239|186801|186802|216572|216851;2|1783272|1239|186801|3085636|186803|1407607;2|1783272|1239|186801|186802|216572|459786;2|976|200643|171549|2005525|375288;2|3379134|1224|28216|80840|995019|40544;2|1783272|1239|526524|526525|2810280|3025755;2|1783272|1239|186801|3085636|186803|2316020|33039;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|3085636|186803|297314;2|1783272|1239|186801|186802|216572|707003,Complete,NA bsdb:1237/1/1,Study 1237,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden KF, Shukla SD, Bowerman KL, Vaughan A, Gellatly SL, Wood DLA, Lachner N, Idrees S, Rehman SF, Faiz A, Patel VK, Donovan C, Alemao CA, Shen S, Amorim N, Majumder R, Vanka KS, Mason J, Haw TJ, Tillet B, Fricker M, Keely S, Hansbro N, Belz GT, Horvat J, Ashhurst T, van Vreden C, McGuire H, Fazekas de St Groth B, King NJC, Crossett B, Cordwell SJ, Bonaguro L, Schultze JL, Hamilton-Williams EE, Mann E, Forster SC, Cooper MA, Segal LN, Chotirmall SH, Collins P, Bowman R, Fong KM, Yang IA, Wark PAB, Dennis PG, Hugenholtz P , Hansbro PM",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed FMT mice - 12 weeks,Cigarette Smoke exposed FMT mice (CS-exposed 12 weeks),"Cigarette Smoke exposed FMT mice (CS-exposed 12 weeks) refers to ""in vivo"" female mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT) who underwent 3 weeks of baseline microbiome normalisation by transferring soiled bedding and co-housing, before exposure to mainstream CS through the nose only for 12 weeks (12 wk CS).",8,8,NA,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Supplementary Table 6,22 November 2024,KateRasheed,KateRasheed,Differential abundant taxa between air-exposed FMT mice and CS-exposed FMT mice at 12 weeks,decreased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Kineothrix|s__Kineothrix sp.,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Muricomes|s__Muricomes sp.,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium 14-2",2|1783272|1239|186801|3085636|186803|2163168|2163169;2|1783272|1239|186801|3085636|186803|1918542|1918608;2|1783272|1239|186801|3085636|186803|397286,Complete,Svetlana up bsdb:1237/1/2,Study 1237,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden KF, Shukla SD, Bowerman KL, Vaughan A, Gellatly SL, Wood DLA, Lachner N, Idrees S, Rehman SF, Faiz A, Patel VK, Donovan C, Alemao CA, Shen S, Amorim N, Majumder R, Vanka KS, Mason J, Haw TJ, Tillet B, Fricker M, Keely S, Hansbro N, Belz GT, Horvat J, Ashhurst T, van Vreden C, McGuire H, Fazekas de St Groth B, King NJC, Crossett B, Cordwell SJ, Bonaguro L, Schultze JL, Hamilton-Williams EE, Mann E, Forster SC, Cooper MA, Segal LN, Chotirmall SH, Collins P, Bowman R, Fong KM, Yang IA, Wark PAB, Dennis PG, Hugenholtz P , Hansbro PM",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 1,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed FMT mice - 12 weeks,Cigarette Smoke exposed FMT mice (CS-exposed 12 weeks),"Cigarette Smoke exposed FMT mice (CS-exposed 12 weeks) refers to ""in vivo"" female mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT) who underwent 3 weeks of baseline microbiome normalisation by transferring soiled bedding and co-housing, before exposure to mainstream CS through the nose only for 12 weeks (12 wk CS).",8,8,NA,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 2,Supplementary Table 6,22 November 2024,KateRasheed,KateRasheed,Differential abundant taxa between air-exposed FMT mice and CS-exposed FMT mice at 12 weeks,increased,"k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia|s__Akkermansia muciniphila,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Candidatus Amulumruptor|s__Candidatus Amulumruptor sp.,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Duncaniella|s__Duncaniella sp.,k__Bacteria|k__Pseudomonadati|p__Thermodesulfobacteriota|c__Desulfovibrionia|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Mailhella|s__Mailhella sp.,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum sp.,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella sp. CAG:485",2|3379134|74201|203494|48461|1647988|239934|239935;2|3379134|976|200643|171549|2005473|2510710|2854024;2|3379134|976|200643|171549|2005473|2518495|2518496;2|3379134|200940|3031449|213115|194924|1981028|1981029;2|3379134|976|200643|171549|2005473|1918540|1918611;2|3379134|976|200643|171549|815|909656|821;2|3379134|976|200643|171549|171552|838|1262927,Complete,Svetlana up bsdb:1237/2/1,Study 1237,randomized controlled trial,38331563,10.1136/gutjnl-2023-330521,NA,"Budden KF, Shukla SD, Bowerman KL, Vaughan A, Gellatly SL, Wood DLA, Lachner N, Idrees S, Rehman SF, Faiz A, Patel VK, Donovan C, Alemao CA, Shen S, Amorim N, Majumder R, Vanka KS, Mason J, Haw TJ, Tillet B, Fricker M, Keely S, Hansbro N, Belz GT, Horvat J, Ashhurst T, van Vreden C, McGuire H, Fazekas de St Groth B, King NJC, Crossett B, Cordwell SJ, Bonaguro L, Schultze JL, Hamilton-Williams EE, Mann E, Forster SC, Cooper MA, Segal LN, Chotirmall SH, Collins P, Bowman R, Fong KM, Yang IA, Wark PAB, Dennis PG, Hugenholtz P , Hansbro PM",Faecal microbial transfer and complex carbohydrates mediate protection against COPD,Gut,2024,"BASIC SCIENCES, COLONIC MICROFLORA, DIETARY FIBRE, IMMUNOLOGY, INFLAMMATORY DISEASES",Experiment 2,Australia,Mus musculus,Feces,UBERON:0001988,Response to transplant,EFO:0007043,Air-exposed FMT mice - 12 weeks,8weeks CS exposed + 4weeks rest FMT mice,8weeks CS exposed + 4weeks rest FMT mice refers to mice who were induced with cigarette-smoke(CS) for 8weeks after which they were exposed to normal air for 4weeks.,8,8,NA,WMS,NA,Illumina,DESeq2,0.05,TRUE,NA,age,NA,NA,unchanged,NA,NA,unchanged,NA,Signature 1,Supplementary Table 6,22 November 2024,KateRasheed,KateRasheed,Differential abundant taxa between 12 weeks air-exposed FMT mice and 8weeks CS exposed + 4weeks rest FMT mice,decreased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes sp.,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus johnsonii,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Muricomes|s__Muricomes sp.,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__Lachnospiraceae bacterium MD335",2|3379134|976|200643|171549|171550|239759|1872444;2|1783272|1239|91061|186826|33958|1578|33959;2|1783272|1239|186801|3085636|186803|1918542|1918608;2|1783272|1239|186801|3085636|186803|1235793,Complete,Svetlana up