From af41cb8c493ac696c1f1a4ae04caa423416bbd21 Mon Sep 17 00:00:00 2001 From: GitHub Actions Bot Date: Tue, 14 Jan 2025 16:01:51 +0000 Subject: [PATCH] Hourly export update --- bugsigdb_signatures_mixed_metaphlan.gmt | 4 +++- bugsigdb_signatures_mixed_ncbi.gmt | 4 +++- bugsigdb_signatures_mixed_taxname.gmt | 4 +++- file_size.csv | 1 + full_dump.csv | 5 +++-- 5 files changed, 13 insertions(+), 5 deletions(-) diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt index 32e6eecc8..7bce139e9 100644 --- a/bugsigdb_signatures_mixed_metaphlan.gmt +++ b/bugsigdb_signatures_mixed_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_15:58_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 @@ -5108,6 +5108,8 @@ bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Ad bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-S)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus 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__Oribacterium k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_DOWN NA k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|k__Thermotogati|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella +bsdb:1086/18/1_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_UP NA k__Bacteria|k__Bacillati|p__Bacillota k__Bacteria|k__Pseudomonadati|p__Campylobacterota k__Bacteria|k__Fusobacteriati|p__Fusobacteriota k__Bacteria k__Bacteria|k__Pseudomonadati|p__Pseudomonadota k__Bacteria|k__Pseudomonadati|p__Spirochaetota +bsdb:1086/18/2_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_DOWN NA k__Bacteria|k__Bacillati|p__Actinomycetota k__Bacteria|k__Pseudomonadati|p__Bacteroidota bsdb:1087/1/4_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Anaerotruncus|s__Anaerotruncus colihominis k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia|s__Blautia producta k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter|s__Gordonibacter urolithinfaciens k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii bsdb:1087/1/5_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_DOWN NA k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia|s__Romboutsia timonensis bsdb:1087/3/1_Treatment-refractory-schizophrenia:TRS:-individuals-with-treatment-resistant-schizophrenia-taking-clozapine_vs_AAP:-individuals-with-treatment-responsive-schizophrenia-taking-atypical-antipsychotics-(not-clozapine)_UP NA k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella|s__Eggerthella lenta k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Eisenbergiella|s__Eisenbergiella tayi k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella|s__Hungatella effluvii k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruthenibacterium|s__Ruthenibacterium lactatiformans diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt index 030af6246..8ba85aa09 100644 --- a/bugsigdb_signatures_mixed_ncbi.gmt +++ b/bugsigdb_signatures_mixed_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_15:58_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 @@ -5108,6 +5108,8 @@ bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Ad bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-S)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA 1654 2801844 194 1016 2717 1716 848 133925 970 195950 bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_UP NA 1283313 1380 1378 724 1164882 482 836 838 1301 29465 265975 508215 bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_DOWN NA 1654 2801844 194 1016 2717 1716 1434006 848 32257 133925 970 195950 +bsdb:1086/18/1_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_UP NA 1239 29547 32066 2 1224 203691 +bsdb:1086/18/2_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_DOWN NA 201174 976 bsdb:1087/1/4_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_UP NA 169435 33035 84112 562 1335613 1096246 bsdb:1087/1/5_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_DOWN NA 1776391 bsdb:1087/3/1_Treatment-refractory-schizophrenia:TRS:-individuals-with-treatment-resistant-schizophrenia-taking-clozapine_vs_AAP:-individuals-with-treatment-responsive-schizophrenia-taking-atypical-antipsychotics-(not-clozapine)_UP NA 84112 1432052 1096246 1550024 diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt index 72b54e806..89a801231 100644 --- a/bugsigdb_signatures_mixed_taxname.gmt +++ b/bugsigdb_signatures_mixed_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_15:58_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 @@ -5108,6 +5108,8 @@ bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Ad bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-S)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA Actinomyces Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Olsenella Selenomonas Tannerella bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Porphyromonas Prevotella Streptococcus Veillonella Oribacterium Rothia bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Children-subgingival-plaque-(PKU-Ch-SP)-patients_vs_Phenylketonuria-Children-Saliva-(PKU-Ch-S)-patients_DOWN NA Actinomyces Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fretibacterium Fusobacterium Kingella Olsenella Selenomonas Tannerella +bsdb:1086/18/1_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_UP NA Bacillota Campylobacterota Fusobacteriota Bacteria Pseudomonadota Spirochaetota +bsdb:1086/18/2_Phenylketonuria:PKU-Rel-S-(related-Phenylketonuria-saliva)-patients_vs_CtrlRel-S-(related-control-saliva)_DOWN NA Actinomycetota Bacteroidota bsdb:1087/1/4_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_UP NA Anaerotruncus colihominis Blautia producta Eggerthella lenta Escherichia coli Gordonibacter urolithinfaciens Hungatella effluvii bsdb:1087/1/5_Schizophrenia:SCZ:-individuals-with-a-psychiatric-diagnosis-of-schizophrenia_vs_control-individuals-without-a-psychiatric-diagnosis-(past-or-present)_DOWN NA Romboutsia timonensis bsdb:1087/3/1_Treatment-refractory-schizophrenia:TRS:-individuals-with-treatment-resistant-schizophrenia-taking-clozapine_vs_AAP:-individuals-with-treatment-responsive-schizophrenia-taking-atypical-antipsychotics-(not-clozapine)_UP NA Eggerthella lenta Eisenbergiella tayi Hungatella effluvii Ruthenibacterium lactatiformans diff --git a/file_size.csv b/file_size.csv index cf24f6621..3d92c2d37 100644 --- a/file_size.csv +++ b/file_size.csv @@ -2536,3 +2536,4 @@ "2025-01-14_13:02_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6669" "6669" "6669" "3012" "3012" "3012" "3012" "3012" "3012" "4497" "7770" "7375" "1368" "2025-01-14_13:58_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6670" "6670" "6670" "3012" "3012" "3012" "3012" "3012" "3012" "4497" "7770" "7375" "1368" "2025-01-14_14:58_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6671" "6671" "6671" "3012" "3012" "3012" "3012" "3012" "3012" "4498" "7771" "7375" "1368" +"2025-01-14_15:58_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6673" "6673" "6673" "3012" "3012" "3012" "3012" "3012" "3012" "4498" "7772" "7377" "1368" diff --git a/full_dump.csv b/full_dump.csv index 9c91d70dd..f58b006c7 100644 --- a/full_dump.csv +++ b/full_dump.csv @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_15:58_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 @@ -6027,7 +6027,8 @@ bsdb:1086/14/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M bsdb:1086/15/NA,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 15,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control No period (CTRL-S),Phenylketonuria No Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) without suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA bsdb:1086/16/NA,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 16,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Control Period (CTRL-S),Phenylketonuria Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) with suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA bsdb:1086/17/NA,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 17,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,Phenylketonuria No Period (PKU-S),Phenylketonuria Period (PKU-S),Patients diagnosed with Phenylketonuria (PKU) with suspected Periodontitis and who stimulated Saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA -bsdb:1086/18/NA,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 18,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,CtrlRel-S (related control saliva),PKU-Rel-S (related Phenylketonuria saliva) patients,Controls related to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,unchanged,NA,NA,NA,increased,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA +bsdb:1086/18/1,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 18,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,CtrlRel-S (related control saliva),PKU-Rel-S (related Phenylketonuria saliva) patients,Controls related to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,unchanged,NA,NA,NA,increased,Signature 1,Appendix Table 4,14 January 2025,Tosin,Tosin,Differential abundant phylum between Ctrl-Rel-S (Control related saliva) patients and PKU-Rel-S (Phenylketonuria related saliva) patients,increased,"k__Bacteria|k__Bacillati|p__Bacillota,k__Bacteria|k__Pseudomonadati|p__Campylobacterota,k__Bacteria|k__Fusobacteriati|p__Fusobacteriota,k__Bacteria,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota,k__Bacteria|k__Pseudomonadati|p__Spirochaetota",2|1783272|1239;2|3379134|29547;2|3384189|32066;2;2|3379134|1224;2|3379134|203691,Complete,NA +bsdb:1086/18/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK , Richter GM",Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study,Journal of clinical periodontology,2024,"16s rDNA sequencing, periodontitis, phenylketonuria, saliva, subgingival plaque",Experiment 18,Germany,Homo sapiens,Saliva,UBERON:0001836,Phenylketonuria,MONDO:0009861,CtrlRel-S (related control saliva),PKU-Rel-S (related Phenylketonuria saliva) patients,Controls related to Phenylketonuria (PKU) patients who stimulated saliva samples were gotten from.,NA,NA,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,decreased,unchanged,NA,NA,NA,increased,Signature 2,Appendix Table 4,14 January 2025,Tosin,Tosin,Differential abundant phylum between Ctrl-Rel-S (Control related saliva) patients and PKU-Rel-S (Phenylketonuria related saliva) patients.,decreased,"k__Bacteria|k__Bacillati|p__Actinomycetota,k__Bacteria|k__Pseudomonadati|p__Bacteroidota",2|1783272|201174;2|3379134|976,Complete,NA bsdb:1087/1/4,Study 1087,case-control,38294805,10.1001/jamapsychiatry.2023.5371,NA,"Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J , Eyles D",Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia,JAMA psychiatry,2024,NA,Experiment 1,Australia,Homo sapiens,Feces,UBERON:0001988,Schizophrenia,MONDO:0005090,control individuals without a psychiatric diagnosis (past or present),SCZ: individuals with a psychiatric diagnosis of schizophrenia,"Participants with a schizophrenia diagnosis categorized as follows: 1. AAP: individuals with treatment-responsive schizophrenia taking atypical antipsychotics (not clozapine) with a total Positive and Negative Symptom Scale (PANSS) score of 60 or low. 2. CR: individuals with treatment-resistant schizophrenia who were clozapine responsive total PANSS score ≤60).