diff --git a/bugsigdb_signatures_genus_metaphlan.gmt b/bugsigdb_signatures_genus_metaphlan.gmt index 84ff45b3b..e845cf41d 100644 --- a/bugsigdb_signatures_genus_metaphlan.gmt +++ b/bugsigdb_signatures_genus_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -3479,7 +3479,7 @@ bsdb:938/3/1_Gut-microbiome-measurement:Colon-of-Tan-Sheep-(T_Co)_vs_Colon-of-Do bsdb:938/4/1_Gut-microbiome-measurement:Rumen-of-Tan-Sheep-(T_R)_vs_Rumen-of-Dorper-sheep-(D_R)_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans bsdb:938/5/1_Gut-microbiome-measurement:Duodenum-of-Tan-Sheep-(T_Du)_vs_Duodenum-of-Dorper-sheep-(D_Du)_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia bsdb:938/7/1_Gut-microbiome-measurement:Colon-of-Tan-Sheep-(T_Co)_vs_Colon-of-Dorper-sheep-(D_Co)_UP NA k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis -bsdb:939/1/1_Irritable-bowel-syndrome:Irritable-Bowel-Syndrome-positive-(IBS+)_vs_Irritable-Bowel-Syndrome-negative-(IBS-)_DOWN 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 +bsdb:939/1/1_Irritable-bowel-syndrome:Irritable-Bowel-Syndrome-positive-(IBS+)_vs_Irritable-Bowel-Syndrome-negative-(IBS-)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella bsdb:940/1/1_COVID-19:Healthy-Controls-Group_vs_Covid-19-and-Post-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea k__Eukaryota|k__Fungi|p__Ascomycota|g__Milospium k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Ophiostoma bsdb:940/2/1_COVID-19:Covid-19-Group_vs_Healthy-Controls-and-Post-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina k__Eukaryota|k__Fungi|c__Entorrhizomycetes|o__Entorrhizales|f__Entorrhizaceae|g__Entorrhiza k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Fuscosporellales|f__Fuscosporellaceae|g__Parafuscosporella k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces bsdb:940/3/1_COVID-19:Post-Covid-19-Group_vs_Healthy-Controls-and-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Botryosphaeria k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Dipodascus k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces @@ -4575,13 +4575,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia 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:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__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:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA 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__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-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__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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 +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-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__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus 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 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia 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 k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Eggerthella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae|g__Gordonibacter k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Hungatella diff --git a/bugsigdb_signatures_genus_metaphlan_exact.gmt b/bugsigdb_signatures_genus_metaphlan_exact.gmt index b8315a86e..6a9247391 100644 --- a/bugsigdb_signatures_genus_metaphlan_exact.gmt +++ b/bugsigdb_signatures_genus_metaphlan_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -2861,7 +2861,7 @@ bsdb:937/1/2_Pregnancy:Clinical-pregnancy-(FP)_vs_Non-pregnant-(FN)_UP NA k__Bac bsdb:938/4/1_Gut-microbiome-measurement:Rumen-of-Tan-Sheep-(T_R)_vs_Rumen-of-Dorper-sheep-(D_R)_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Papillibacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans bsdb:938/5/1_Gut-microbiome-measurement:Duodenum-of-Tan-Sheep-(T_Du)_vs_Duodenum-of-Dorper-sheep-(D_Du)_UP NA k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Saccharofermentans k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Senegalimassilia bsdb:938/7/1_Gut-microbiome-measurement:Colon-of-Tan-Sheep-(T_Co)_vs_Colon-of-Dorper-sheep-(D_Co)_UP NA k__Bacteria|p__Lentisphaerota|c__Lentisphaeria|o__Victivallales|f__Victivallaceae|g__Victivallis -bsdb:939/1/1_Irritable-bowel-syndrome:Irritable-Bowel-Syndrome-positive-(IBS+)_vs_Irritable-Bowel-Syndrome-negative-(IBS-)_DOWN 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 +bsdb:939/1/1_Irritable-bowel-syndrome:Irritable-Bowel-Syndrome-positive-(IBS+)_vs_Irritable-Bowel-Syndrome-negative-(IBS-)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella bsdb:940/1/1_COVID-19:Healthy-Controls-Group_vs_Covid-19-and-Post-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea k__Eukaryota|k__Fungi|p__Ascomycota|g__Milospium k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Ophiostoma bsdb:940/2/1_COVID-19:Covid-19-Group_vs_Healthy-Controls-and-Post-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina k__Eukaryota|k__Fungi|c__Entorrhizomycetes|o__Entorrhizales|f__Entorrhizaceae|g__Entorrhiza k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Fuscosporellales|f__Fuscosporellaceae|g__Parafuscosporella k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces bsdb:940/3/1_COVID-19:Post-Covid-19-Group_vs_Healthy-Controls-and-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Botryosphaeria k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Dipodascus k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces @@ -3830,13 +3830,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia 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:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__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:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA 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__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-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__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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 +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-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__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus 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 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia bsdb:1088/1/1_Schizophrenia:SCZF:-patients-with-schizophrenia_vs_HCF:-healthy-controls-(no-psychiatric-diagnosis-of-schizophrenia)_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Arthrobacter k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Cupriavidus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Leptothrix k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Rhizobiaceae|g__Mycoplana k__Bacteria|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Pseudochrobactrum k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Pseudoramibacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Shigella diff --git a/bugsigdb_signatures_genus_ncbi.gmt b/bugsigdb_signatures_genus_ncbi.gmt index 73203dde7..73bf7019e 100644 --- a/bugsigdb_signatures_genus_ncbi.gmt +++ b/bugsigdb_signatures_genus_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -4575,13 +4575,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 1164882 bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 32257 32067 133925 970 195950 bsdb:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 32257 133925 970 195950 -bsdb:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA 838 265975 836 482 1283313 1380 1378 724 1257 1213720 1301 29465 -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA 1016 848 1716 32257 2801844 2717 133925 195950 194 1434006 -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA 1283313 1380 1378 724 1164882 482 265975 1257 836 838 508215 1213720 1301 29465 -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA 1654 416916 2801844 194 1016 2717 1716 1434006 848 32257 47670 133925 2740 970 195950 -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA 838 508215 1164882 1283313 1380 1378 724 1213720 1301 29465 -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA 194 2740 133925 2717 1654 970 2801844 1434006 1716 848 1016 +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 970 195950 +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA 2801844 194 1016 2717 1716 848 195950 970 416916 +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_UP NA 1283313 1380 1378 724 1164882 482 265975 1257 836 838 508215 1213720 1301 29465 +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_DOWN NA 1654 2801844 194 1016 2717 1716 1434006 848 32257 2740 970 195950 133925 +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA 838 508215 1164882 1283313 1380 1378 724 1213720 1301 29465 +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA 194 2740 133925 2717 1654 970 2801844 1434006 1716 848 1016 bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA 1283313 1380 1378 724 1164882 482 1257 836 838 1301 29465 bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA 194 195950 2740 133925 2717 1654 970 32257 1434006 1716 848 1016 2801844 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 244127 572511 84111 561 644652 1649459 diff --git a/bugsigdb_signatures_genus_ncbi_exact.gmt b/bugsigdb_signatures_genus_ncbi_exact.gmt index 6fd1b4ff2..cce4f38b7 100644 --- a/bugsigdb_signatures_genus_ncbi_exact.gmt +++ b/bugsigdb_signatures_genus_ncbi_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -3830,13 +3830,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 1164882 bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 32257 32067 133925 970 195950 bsdb:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 32257 133925 970 195950 -bsdb:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA 838 265975 836 482 1283313 1380 1378 724 1257 1213720 1301 29465 -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA 1016 848 1716 32257 2801844 2717 133925 195950 194 1434006 -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA 1283313 1380 1378 724 1164882 482 265975 1257 836 838 508215 1213720 1301 29465 -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA 1654 416916 2801844 194 1016 2717 1716 1434006 848 32257 47670 133925 2740 970 195950 -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA 838 508215 1164882 1283313 1380 1378 724 1213720 1301 29465 -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA 194 2740 133925 2717 1654 970 2801844 1434006 1716 848 1016 +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 970 195950 +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA 2801844 194 1016 2717 1716 848 195950 970 416916 +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_UP NA 1283313 1380 1378 724 1164882 482 265975 1257 836 838 508215 1213720 1301 29465 +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_DOWN NA 1654 2801844 194 1016 2717 1716 1434006 848 32257 2740 970 195950 133925 +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA 838 508215 1164882 1283313 1380 1378 724 1213720 1301 29465 +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA 194 2740 133925 2717 1654 970 2801844 1434006 1716 848 1016 bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA 1283313 1380 1378 724 1164882 482 1257 836 838 1301 29465 bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA 194 195950 2740 133925 2717 1654 970 32257 1434006 1716 848 1016 2801844 bsdb:1088/1/1_Schizophrenia:SCZF:-patients-with-schizophrenia_vs_HCF:-healthy-controls-(no-psychiatric-diagnosis-of-schizophrenia)_UP NA 1654 1663 102106 106589 1730 88 13159 354349 286 113286 620 diff --git a/bugsigdb_signatures_genus_taxname.gmt b/bugsigdb_signatures_genus_taxname.gmt index 201c4fe6c..48fa0bec9 100644 --- a/bugsigdb_signatures_genus_taxname.gmt +++ b/bugsigdb_signatures_genus_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -4575,13 +4575,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia Lachnoanaerobaculum bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Kingella Leptotrichia Olsenella Selenomonas Tannerella bsdb:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Kingella Olsenella Selenomonas Tannerella -bsdb:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA Prevotella Oribacterium Porphyromonas Neisseria Alloprevotella Atopobium Gemella Haemophilus Peptostreptococcus Stomatobaculum Streptococcus Veillonella -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA Capnocytophaga Fusobacterium Corynebacterium Kingella Arachnia Cardiobacterium Olsenella Tannerella Campylobacter Fretibacterium -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Rothia Stomatobaculum Streptococcus Veillonella -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA Actinomyces Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fretibacterium Fusobacterium Kingella Lautropia Olsenella Peptococcus Selenomonas Tannerella -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA Prevotella Rothia Lachnoanaerobaculum Alloprevotella Atopobium Gemella Haemophilus Stomatobaculum Streptococcus Veillonella -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA Campylobacter Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Arachnia Fretibacterium Corynebacterium Fusobacterium Capnocytophaga +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Selenomonas Tannerella +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Tannerella Selenomonas Aggregatibacter +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Rothia Stomatobaculum Streptococcus Veillonella +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_DOWN NA Actinomyces Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fretibacterium Fusobacterium Kingella Peptococcus Selenomonas Tannerella Olsenella +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA Prevotella Rothia Lachnoanaerobaculum Alloprevotella Atopobium Gemella Haemophilus Stomatobaculum Streptococcus Veillonella +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA Campylobacter Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Arachnia Fretibacterium Corynebacterium Fusobacterium Capnocytophaga bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Peptostreptococcus Porphyromonas Prevotella Streptococcus Veillonella bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA Campylobacter Tannerella Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Kingella Fretibacterium Corynebacterium Fusobacterium Capnocytophaga Arachnia 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 Blautia Eggerthella Escherichia Gordonibacter Hungatella diff --git a/bugsigdb_signatures_genus_taxname_exact.gmt b/bugsigdb_signatures_genus_taxname_exact.gmt index 7905dd4e0..dd84ed1f9 100644 --- a/bugsigdb_signatures_genus_taxname_exact.gmt +++ b/bugsigdb_signatures_genus_taxname_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -3830,13 +3830,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia Lachnoanaerobaculum bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Kingella Leptotrichia Olsenella Selenomonas Tannerella bsdb:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Kingella Olsenella Selenomonas Tannerella -bsdb:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA Prevotella Oribacterium Porphyromonas Neisseria Alloprevotella Atopobium Gemella Haemophilus Peptostreptococcus Stomatobaculum Streptococcus Veillonella -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA Capnocytophaga Fusobacterium Corynebacterium Kingella Arachnia Cardiobacterium Olsenella Tannerella Campylobacter Fretibacterium -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Rothia Stomatobaculum Streptococcus Veillonella -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA Actinomyces Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fretibacterium Fusobacterium Kingella Lautropia Olsenella Peptococcus Selenomonas Tannerella -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA Prevotella Rothia Lachnoanaerobaculum Alloprevotella Atopobium Gemella Haemophilus Stomatobaculum Streptococcus Veillonella -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA Campylobacter Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Arachnia Fretibacterium Corynebacterium Fusobacterium Capnocytophaga +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Selenomonas Tannerella +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Tannerella Selenomonas Aggregatibacter +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Rothia Stomatobaculum Streptococcus Veillonella +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_DOWN NA Actinomyces Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fretibacterium Fusobacterium Kingella Peptococcus Selenomonas Tannerella Olsenella +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA Prevotella Rothia Lachnoanaerobaculum Alloprevotella Atopobium Gemella Haemophilus Stomatobaculum Streptococcus Veillonella +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA Campylobacter Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Arachnia Fretibacterium Corynebacterium Fusobacterium Capnocytophaga bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Peptostreptococcus Porphyromonas Prevotella Streptococcus Veillonella bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA Campylobacter Tannerella Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Kingella Fretibacterium Corynebacterium Fusobacterium Capnocytophaga Arachnia bsdb:1088/1/1_Schizophrenia:SCZF:-patients-with-schizophrenia_vs_HCF:-healthy-controls-(no-psychiatric-diagnosis-of-schizophrenia)_UP NA Actinomyces Arthrobacter Collinsella Cupriavidus Eubacterium Leptothrix Mycoplana Pseudochrobactrum Pseudomonas Pseudoramibacter Shigella diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt index fe78cce0f..ffde7b23e 100644 --- a/bugsigdb_signatures_mixed_metaphlan.gmt +++ b/bugsigdb_signatures_mixed_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -3900,7 +3900,7 @@ bsdb:938/7/1_Gut-microbiome-measurement:Colon-of-Tan-Sheep-(T_Co)_vs_Colon-of-Do bsdb:938/7/2_Gut-microbiome-measurement:Colon-of-Tan-Sheep-(T_Co)_vs_Colon-of-Dorper-sheep-(D_Co)_DOWN NA k__Bacteria k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium bsdb:938/8/1_Gut-microbiome-measurement:Cecum-of-Tan-Sheep-(T_C)_vs_Cecum-of-Dorper-sheep-(D_C)_UP NA k__Bacteria|p__Pseudomonadota k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium bsdb:938/8/2_Gut-microbiome-measurement:Cecum-of-Tan-Sheep-(T_C)_vs_Cecum-of-Dorper-sheep-(D_C)_DOWN NA k__Bacteria|p__Actinomycetota -bsdb:939/1/1_Irritable-bowel-syndrome:Irritable-Bowel-Syndrome-positive-(IBS+)_vs_Irritable-Bowel-Syndrome-negative-(IBS-)_DOWN 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 +bsdb:939/1/1_Irritable-bowel-syndrome:Irritable-Bowel-Syndrome-positive-(IBS+)_vs_Irritable-Bowel-Syndrome-negative-(IBS-)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae bsdb:940/1/1_COVID-19:Healthy-Controls-Group_vs_Covid-19-and-Post-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis|s__Arthrographis grakistii k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola k__Eukaryota|k__Fungi|p__Ascomycota|g__Milospium|s__Milospium graphideorum k__Eukaryota|k__Fungi|p__Ascomycota|g__Milospium k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium kenpeggii k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula|s__Russula xerophila k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus amstelodami k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Ophiostoma bsdb:940/2/1_COVID-19:Covid-19-Group_vs_Healthy-Controls-and-Post-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys|s__Acrodictys fluminicola k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus subflavus k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria|s__Chrysosphaeria jannelii k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina|s__Angustimassarina camporesii k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium|s__Simplicillium sympodiophorum k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina k__Eukaryota|k__Fungi|c__Entorrhizomycetes|o__Entorrhizales|f__Entorrhizaceae|g__Entorrhiza k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella|s__Parasympodiella longispora k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber|s__Tuber alcaracense k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces|s__Fantasmomyces hyalinus k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Fuscosporellales|f__Fuscosporellaceae|g__Parafuscosporella k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|s__[Cryptococcus] ater k__Eukaryota|k__Fungi|p__Ascomycota|g__Vanakripa|s__Vanakripa mucosa k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces bsdb:940/3/1_COVID-19:Post-Covid-19-Group_vs_Healthy-Controls-and-Covid-19-Groups_UP NA k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor|s__Actinomucor elegans k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus versicolor k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Botryosphaeria k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Dipodascus k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum pseudocandidum k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum candidum k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor circinelloides k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor pseudolusitanicus k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces scorteus k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces megalosporus k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces pyricola @@ -5099,13 +5099,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia 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:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__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:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter 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__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA 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__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-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__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus 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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum 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 +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-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__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus 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 k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia 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 @@ -5555,6 +5555,7 @@ bsdb:1163/2/2_HIV-infection:HIV-positive-(cART)_vs_non-infected-volunteers-(Cont bsdb:1163/3/1_HIV-infection:NRTIs-+-PIs_vs_non-infected-volunteers-(Control)_UP NA k__Bacteria|k__Bacillati|p__Actinomycetota bsdb:1163/3/2_HIV-infection:NRTIs-+-PIs_vs_non-infected-volunteers-(Control)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota bsdb:1163/4/1_HIV-infection:NRTIs-+-NNRTIs_vs_non-infected-volunteers-(C0ntrol)_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota +bsdb:1163/5/2_HIV-infection:NRTIs-+-INSTIs_vs_Non-infected-volunteers-(Control)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota bsdb:1163/6/1_HIV-infection:NRTIs+PIs_vs_non-infected-volunteers-(Control)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae 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__Flavonifractor|s__Flavonifractor plautii bsdb:1163/6/2_HIV-infection:NRTIs+PIs_vs_non-infected-volunteers-(Control)_DOWN NA k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium bsdb:1163/7/1_HIV-infection:NRTIs-+-NNRTIs_vs_non-infected-volunteers-(Control)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium 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 k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt index a1f00215a..32ca111fa 100644 --- a/bugsigdb_signatures_mixed_ncbi.gmt +++ b/bugsigdb_signatures_mixed_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -5099,13 +5099,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 1164882 bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 32257 32067 133925 970 195950 bsdb:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 32257 133925 970 195950 -bsdb:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA 838 265975 836 482 1283313 1380 1378 724 1257 1213720 1301 29465 -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA 1016 848 1716 32257 2801844 2717 133925 195950 194 1434006 -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA 1283313 1380 1378 724 1164882 482 265975 1257 836 838 508215 1213720 1301 29465 -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA 1654 416916 2801844 194 1016 2717 1716 1434006 848 32257 47670 133925 2740 970 195950 -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA 838 508215 1164882 1283313 1380 1378 724 1213720 1301 29465 -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA 194 2740 133925 2717 1654 970 2801844 1434006 1716 848 1016 +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA 416916 2801844 194 1016 2717 1716 848 970 195950 +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_UP NA 1283313 1380 1378 724 482 265975 1257 836 838 1213720 1301 29465 508215 +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA 2801844 194 1016 2717 1716 848 195950 970 416916 +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_UP NA 1283313 1380 1378 724 1164882 482 265975 1257 836 838 508215 1213720 1301 29465 +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_DOWN NA 1654 2801844 194 1016 2717 1716 1434006 848 32257 2740 970 195950 133925 +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA 838 508215 1164882 1283313 1380 1378 724 1213720 1301 29465 +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA 194 2740 133925 2717 1654 970 2801844 1434006 1716 848 1016 bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA 1283313 1380 1378 724 1164882 482 1257 836 838 1301 29465 bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA 194 195950 2740 133925 2717 1654 970 32257 1434006 1716 848 1016 2801844 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 @@ -5555,6 +5555,7 @@ bsdb:1163/2/2_HIV-infection:HIV-positive-(cART)_vs_non-infected-volunteers-(Cont bsdb:1163/3/1_HIV-infection:NRTIs-+-PIs_vs_non-infected-volunteers-(Control)_UP NA 201174 bsdb:1163/3/2_HIV-infection:NRTIs-+-PIs_vs_non-infected-volunteers-(Control)_DOWN NA 1239 bsdb:1163/4/1_HIV-infection:NRTIs-+-NNRTIs_vs_non-infected-volunteers-(C0ntrol)_UP NA 1224 +bsdb:1163/5/2_HIV-infection:NRTIs-+-INSTIs_vs_Non-infected-volunteers-(Control)_DOWN NA 1239 bsdb:1163/6/1_HIV-infection:NRTIs+PIs_vs_non-infected-volunteers-(Control)_UP NA 1898207 186803 84111 292800 bsdb:1163/6/2_HIV-infection:NRTIs+PIs_vs_non-infected-volunteers-(Control)_DOWN NA 2037 72274 204457 171552 838 123375 bsdb:1163/7/1_HIV-infection:NRTIs-+-NNRTIs_vs_non-infected-volunteers-(Control)_UP NA 1288121 2212467 2030927 84107 84999 186803 286 1301 diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt index d4f127a81..7079429bf 100644 --- a/bugsigdb_signatures_mixed_taxname.gmt +++ b/bugsigdb_signatures_mixed_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -5099,13 +5099,13 @@ bsdb:1086/8/2_Phenylketonuria:ChPKU-S-(PKU-children-saliva)-patients_vs_ChCtrlRe bsdb:1086/9/1_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia Lachnoanaerobaculum bsdb:1086/9/2_Phenylketonuria:Control-Subgingival-plaque-(Ctrl-SP)-patients_vs_Control-Saliva-(Ctrl-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Kingella Leptotrichia Olsenella Selenomonas Tannerella bsdb:1086/10/1_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia -bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Kingella Olsenella Selenomonas Tannerella -bsdb:1086/11/1_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_UP NA Prevotella Oribacterium Porphyromonas Neisseria Alloprevotella Atopobium Gemella Haemophilus Peptostreptococcus Stomatobaculum Streptococcus Veillonella -bsdb:1086/11/2_Phenylketonuria:Control-Children-(CTRL-Ch-SP)_vs_Control-Children-(CTRL-Ch-S)_DOWN NA Capnocytophaga Fusobacterium Corynebacterium Kingella Arachnia Cardiobacterium Olsenella Tannerella Campylobacter Fretibacterium -bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Rothia Stomatobaculum Streptococcus Veillonella -bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-(PKU-SP)_vs_Phenylketonuria-(PKU-S)_DOWN NA Actinomyces Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fretibacterium Fusobacterium Kingella Lautropia Olsenella Peptococcus Selenomonas Tannerella -bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_UP NA Prevotella Rothia Lachnoanaerobaculum Alloprevotella Atopobium Gemella Haemophilus Stomatobaculum Streptococcus Veillonella -bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-(PKU-SP)_vs_Phenylketonuria-Adults-(PKU-S)_DOWN NA Campylobacter Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Arachnia Fretibacterium Corynebacterium Fusobacterium Capnocytophaga +bsdb:1086/10/2_Phenylketonuria:Control-Adults-Subgingival-plaque-(Ctrl-Adults-SP)-patients_vs_Control-Adults-Saliva-(Ctrl-Adults-S)-patients_DOWN NA Aggregatibacter Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Selenomonas Tannerella +bsdb:1086/11/1_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Stomatobaculum Streptococcus Veillonella Rothia +bsdb:1086/11/2_Phenylketonuria:Control-Children-Subgingival-plaque-(Ctrl-Ch-SP)-patients_vs_Control-Children-Saliva-(Ctrl-Ch-S)-patients_DOWN NA Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fusobacterium Tannerella Selenomonas Aggregatibacter +bsdb:1086/12/1_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Oribacterium Peptostreptococcus Porphyromonas Prevotella Rothia Stomatobaculum Streptococcus Veillonella +bsdb:1086/12/2_Phenylketonuria:Phenylketonuria-Subgingival-plaque-(PKU-SP)-patients_vs_Phenylketonuria-Saliva-(PKU-S)-patients_DOWN NA Actinomyces Arachnia Campylobacter Capnocytophaga Cardiobacterium Corynebacterium Fretibacterium Fusobacterium Kingella Peptococcus Selenomonas Tannerella Olsenella +bsdb:1086/13/1_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_UP NA Prevotella Rothia Lachnoanaerobaculum Alloprevotella Atopobium Gemella Haemophilus Stomatobaculum Streptococcus Veillonella +bsdb:1086/13/2_Phenylketonuria:Phenylketonuria-Adults-Subgingival-plaque-(PKU-Adults-SP)_vs_Phenylketonuria-Adults-Saliva-(PKU-Adults-S)_DOWN NA Campylobacter Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Arachnia Fretibacterium Corynebacterium Fusobacterium Capnocytophaga bsdb:1086/14/1_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_UP NA Alloprevotella Atopobium Gemella Haemophilus Lachnoanaerobaculum Neisseria Peptostreptococcus Porphyromonas Prevotella Streptococcus Veillonella bsdb:1086/14/2_Phenylketonuria:Phenylketonuria-Ch-(PKU-SP)_vs_Phenylketonuria-Ch-(PKU-S)_DOWN NA Campylobacter Tannerella Peptococcus Olsenella Cardiobacterium Actinomyces Selenomonas Kingella Fretibacterium Corynebacterium Fusobacterium Capnocytophaga Arachnia 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 @@ -5555,6 +5555,7 @@ bsdb:1163/2/2_HIV-infection:HIV-positive-(cART)_vs_non-infected-volunteers-(Cont bsdb:1163/3/1_HIV-infection:NRTIs-+-PIs_vs_non-infected-volunteers-(Control)_UP NA Actinomycetota bsdb:1163/3/2_HIV-infection:NRTIs-+-PIs_vs_non-infected-volunteers-(Control)_DOWN NA Bacillota bsdb:1163/4/1_HIV-infection:NRTIs-+-NNRTIs_vs_non-infected-volunteers-(C0ntrol)_UP NA Pseudomonadota +bsdb:1163/5/2_HIV-infection:NRTIs-+-INSTIs_vs_Non-infected-volunteers-(Control)_DOWN NA Bacillota bsdb:1163/6/1_HIV-infection:NRTIs+PIs_vs_non-infected-volunteers-(Control)_UP NA Clostridiales bacterium Lachnospiraceae Eggerthella Flavonifractor plautii bsdb:1163/6/2_HIV-infection:NRTIs+PIs_vs_non-infected-volunteers-(Control)_DOWN NA Actinomycetales Pseudomonadales Sphingomonadales Prevotellaceae Prevotella Solobacterium bsdb:1163/7/1_HIV-infection:NRTIs-+-NNRTIs_vs_non-infected-volunteers-(Control)_UP NA Alistipes senegalensis Bacteroidaceae bacterium Bacteroidales bacterium Coriobacteriaceae Coriobacteriales Lachnospiraceae Pseudomonas Streptococcus diff --git a/file_size.csv b/file_size.csv index 118364fdc..bf293786b 100644 --- a/file_size.csv +++ b/file_size.csv @@ -2534,3 +2534,4 @@ "2025-01-14_10:58_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6664" "6664" "6664" "3012" "3012" "3012" "3012" "3012" "3012" "4497" "7770" "7375" "1368" "2025-01-14_11:58_UTC" "4898" "5742" "4898" "5742" "4898" "5742" "6667" "6667" "6667" "3012" "3012" "3012" "3012" "3012" "3012" "4497" "7770" "7375" "1368" "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" diff --git a/full_dump.csv b/full_dump.csv index 28e0a2741..9b0720d1a 100644 --- a/full_dump.csv +++ b/full_dump.csv @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-14_13:02_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-14_13:58_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 @@ -4528,7 +4528,7 @@ bsdb:938/7/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2 bsdb:938/7/2,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 7,China,Ovis aries,Colon,UBERON:0001155,Gut microbiome measurement,EFO:0007874,Colon of Dorper sheep (D_Co),Colon of Tan Sheep (T_Co),"Colon of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Fig. S9,11 April 2024,Scholastica,Scholastica,LEfSe analysis of colonic microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,decreased,"k__Bacteria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__uncultured Bacteroidales bacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|s__uncultured Lachnospiraceae bacterium",2;2|976|200643|171549|171550;2|976|200643|171549|194843;2|1239|186801|3085636|186803|297314,Complete,Svetlana up bsdb:938/8/1,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 8,China,Ovis aries,Caecum,UBERON:0001153,Gut microbiome measurement,EFO:0007874,Cecum of Dorper sheep (D_C),Cecum of Tan Sheep (T_C),"Cecum of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Fig. S10,11 April 2024,Scholastica,Scholastica,LEfSe analysis of cecal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,increased,"k__Bacteria|p__Pseudomonadota,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|s__uncultured Oscillospiraceae bacterium",2|1224;2|1239|186801|186802|216572|707003,Complete,Svetlana up bsdb:938/8/2,Study 938,laboratory experiment,37936065,10.1186/s12866-023-03079-2,NA,"Li Z, Cui R, Wang YB, Luo YB, Xue PX, Tang QG , Fang MY",Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle,BMC microbiology,2023,"16S rDNA, Gut microbiota, Metagenomics, Tan sheep",Experiment 8,China,Ovis aries,Caecum,UBERON:0001153,Gut microbiome measurement,EFO:0007874,Cecum of Dorper sheep (D_C),Cecum of Tan Sheep (T_C),"Cecum of Tan sheep bred in Ningxia, China",6,6,No antibiotics during the experiment period,16S,34,Illumina,LEfSe,0.05,TRUE,2,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Fig. S10,11 April 2024,Scholastica,Scholastica,LEfSe analysis of cecal microbiota in Tan sheep versus Dorper sheep from 16S data at the genus level.,decreased,k__Bacteria|p__Actinomycetota,2|201174,Complete,Svetlana up -bsdb:939/1/1,Study 939,case-control,28891262,10.1111/ene.13398,https://pubmed.ncbi.nlm.nih.gov/28891262/,"Mertsalmi TH, Aho VTE, Pereira PAB, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",More than constipation - bowel symptoms in Parkinson's disease and their connection to gut microbiota,European journal of neurology,2017,"Parkinson's disease, constipation, irritable bowel syndrome, microbiota, non-motor symptoms",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Irritable Bowel Syndrome negative (IBS-),Irritable Bowel Syndrome positive (IBS+),Parkinson’s Disease patients with Irritable Bowel Syndrome (IBS)-like symptoms.,56,18,One month.,16S,123,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,18 April 2024,Abiola-Salako,Abiola-Salako,Bacteria with significant differences in relative abundance between PD Patients with or without IBS-like symptoms,decreased,"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",2|976|200643|171549|815|816;2|976|200643|171549|171552|838;2|976|200643|171549|171552,Complete,NA +bsdb:939/1/1,Study 939,case-control,28891262,10.1111/ene.13398,https://pubmed.ncbi.nlm.nih.gov/28891262/,"Mertsalmi TH, Aho VTE, Pereira PAB, Paulin L, Pekkonen E, Auvinen P , Scheperjans F",More than constipation - bowel symptoms in Parkinson's disease and their connection to gut microbiota,European journal of neurology,2017,"Parkinson's disease, constipation, irritable bowel syndrome, microbiota, non-motor symptoms",Experiment 1,Finland,Homo sapiens,Feces,UBERON:0001988,Irritable bowel syndrome,EFO:0000555,Irritable Bowel Syndrome negative (IBS-),Irritable Bowel Syndrome positive (IBS+),Parkinson’s Disease patients with Irritable Bowel Syndrome (IBS)-like symptoms.,56,18,One month.,16S,123,Roche454,DESeq2,0.05,TRUE,NA,NA,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 1,18 April 2024,Abiola-Salako,Abiola-Salako,Bacteria with significant differences in relative abundance between PD Patients with or without IBS-like symptoms,decreased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae",2|3379134|976|200643|171549|815|816;2|3379134|976|200643|171549|171552|838;2|3379134|976|200643|171549|171552,Complete,ChiomaBlessing bsdb:940/1/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 1,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Covid-19 and Post Covid-19 Groups,Healthy Controls Group,Participants in this group were 132 age- and sex-matched healthy individuals (controls),93,132,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,19 April 2024,Victoria,"Victoria,Aleru Divine","This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora|s__Zanclospora jonesii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Chaetosphaeriales|f__Chaetosphaeriaceae|g__Zanclospora,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Tremellales|f__Cryptococcaceae|g__Cryptococcus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Trichosporonales|f__Trichosporonaceae|g__Vanrija|s__Vanrija longa,k__Eukaryota|k__Fungi|p__Ascomycota|c__Leotiomycetes|o__Erysiphales|f__Erysiphaceae|g__Blumeria,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora|s__Diversispora spurca,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Glomeromycetes|o__Diversisporales|f__Diversisporaceae|g__Diversispora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Eremomycetales|f__Eremomycetaceae|g__Arthrographis|s__Arthrographis grakistii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Raffaelea,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Harringtonia|s__Harringtonia lauricola,k__Eukaryota|k__Fungi|p__Ascomycota|g__Milospium|s__Milospium graphideorum,k__Eukaryota|k__Fungi|p__Ascomycota|g__Milospium,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia|s__Malassezia restricta,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Cladosporiales|f__Cladosporiaceae|g__Cladosporium|s__Cladosporium kenpeggii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Agaricomycetes|o__Russulales|f__Russulaceae|g__Russula|s__Russula xerophila,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Diaporthales|f__Diaporthaceae|g__Diaporthe,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida parapsilosis,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus amstelodami,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Ophiostoma",2759|4751|4890|147550|261460|103886|1323519|2040582;2759|4751|4890|147550|261460|103886|1323519;2759|4751|5204|155616|5234|1884633|5206;2759|4751|5204|155616|1851469|1759442|1851468|181171;2759|4751|4890|147548|5120|34371|34372;2759|4751|1913637|214506|214509|308925|308926|308927;2759|4751|1913637|214506|214509|308925|308926;2759|4751|4890|147541|2714147|241722|241727;2759|4751|4890|147541|2714147|241722|241727|2682943;2759|4751|4890|147550|5151|5152|45340;2759|4751|4890|147550|5151|5152|2933754|483707;2759|4751|4890|1666919|1664392;2759|4751|4890|1666919;2759|4751|5204|1538075|162474|742845|55193|76775;2759|4751|4890|147541|2726946|452563|5498|2016221;2759|4751|4890|147545|5042|28568|5094;2759|4751|5204|155619|452342|5401|5402;2759|4751|5204|155619|452342|5401|5402|278596;2759|4751|4890|147550|5114|767018|36922;2759|4751|4890|3239874|2916678|766764|5475|5480;2759|4751|4890|147545|5042|1131492|5052|5054;2759|4751|4890|147550|5151|5152|5159,Complete,Svetlana up bsdb:940/2/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 2,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy Controls and Post-Covid-19 Groups,Covid-19 Group,Participants in this group were COVID-19 patients.,154,71,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,19 April 2024,Victoria,Victoria,"This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Acrodictys|s__Acrodictys fluminicola,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus subflavus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria|s__Chrysosphaeria jannelii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Ophiostomatales|f__Ophiostomataceae|g__Chrysosphaeria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Pezizaceae|g__Hydnobolites|s__Hydnobolites roseus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces cerevisiae,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina|s__Angustimassarina camporesii,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium|s__Simplicillium sympodiophorum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Hypocreales|f__Cordycipitaceae|g__Simplicillium,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Pleosporales|f__Amorosiaceae|g__Angustimassarina,k__Eukaryota|k__Fungi|c__Entorrhizomycetes|o__Entorrhizales|f__Entorrhizaceae|g__Entorrhiza,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella|s__Parasympodiella longispora,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber|s__Tuber alcaracense,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces|s__Fantasmomyces hyalinus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|g__Fantasmomyces,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Coronophorales|f__Scortechiniaceae|g__Parasympodiella,k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Fuscosporellales|f__Fuscosporellaceae|g__Parafuscosporella,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Filobasidiales|f__Filobasidiaceae|s__[Cryptococcus] ater,k__Eukaryota|k__Fungi|p__Ascomycota|g__Vanakripa|s__Vanakripa mucosa,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pezizomycetes|o__Pezizales|f__Tuberaceae|g__Tuber,k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces",2759|4751|4890|147550|1827388;2759|4751|4890|147550|1827388|2571388;2759|4751|4890|147545|5042|1131492|5052|2175223;2759|4751|4890|147550|5151|5152|2875642|2745882;2759|4751|4890|147550|5151|5152|2875642;2759|4751|4890|147549|5185|5186|405928;2759|4751|4890|147549|5185|5186|405928|2489165;2759|4751|4890|4891|4892|4893|4930|4932;2759|4751|4890|147541|92860|1859218|1762950|2599739;2759|4751|4890|147550|5125|474943|292631|935215;2759|4751|4890|147550|5125|474943|292631;2759|4751|4890|147541|92860|1859218|1762950;2759|4751|62907|62910|62911|63255;2759|4751|4890|147550|252166|307582|673167|756022;2759|4751|4890|147549|5185|40289|36048|2698902;2759|4751|4890|147550|1932873|1925498;2759|4751|4890|147550|1932873;2759|4751|4890|147550|252166|307582|673167;2759|4751|4890|147550|1963390|1963370|1963373;2759|4751|5204|155616|90886|5408|104670;2759|4751|4890|2081268|1963375;2759|4751|4890|147549|5185|40289|36048;2759|4751|4890|4891|4892|4893|4930,Complete,Svetlana up bsdb:940/3/1,Study 940,prospective cohort,37119437,10.1002/advs.202205058,https://pmc.ncbi.nlm.nih.gov/articles/PMC10323652/,"Hu X, Wang H, Yu B, Yu J, Lu H, Sun J, Sun Y, Zou Y, Luo H, Zeng Z, Liu S, Jiang Y, Wu Z , Ren Z",Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients,"Advanced science (Weinheim, Baden-Wurttemberg, Germany)",2023,"coronavirus disease 2019, mycobiome, non-invasive biomarkers, oral fungi, severe acute respiratory syndrome coronavirus 2",Experiment 3,China,Homo sapiens,Surface of tongue,UBERON:0007367,COVID-19,MONDO:0100096,Healthy Controls and Covid-19 Groups,Post-Covid-19 Group,This group consists of 22 patients who have recovered from Covid-19.,203,22,8 weeks,ITS / ITS2,NA,Illumina,LEfSe,0.05,FALSE,3,"age,sex",NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 4g,24 April 2024,Victoria,Victoria,"This figure shows the predominant oral fungal among the COVID-19, Post-COVID-19, and control groups.",increased,"k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Actinomucor|s__Actinomucor elegans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus penicillioides,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus versicolor,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dothideomycetes|o__Botryosphaeriales|f__Botryosphaeriaceae|g__Botryosphaeria,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida,k__Eukaryota|k__Fungi|p__Ascomycota|c__Pichiomycetes|o__Serinales|f__Debaryomycetaceae|g__Candida|s__Candida albicans,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Dipodascus,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum pseudocandidum,k__Eukaryota|k__Fungi|p__Ascomycota|c__Dipodascomycetes|o__Dipodascales|f__Dipodascaceae|g__Geotrichum|s__Geotrichum candidum,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Malasseziomycetes|o__Malasseziales|f__Malasseziaceae|g__Malassezia,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor circinelloides,k__Eukaryota|k__Fungi|p__Mucoromycota|c__Mucoromycetes|o__Mucorales|f__Mucoraceae|g__Mucor|s__Mucor pseudolusitanicus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Microbotryomycetes|o__Sporidiobolales|f__Sporidiobolaceae|g__Rhodotorula|s__Rhodotorula mucilaginosa,k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Trichocomaceae|g__Talaromyces|s__Talaromyces scorteus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces megalosporus,k__Eukaryota|k__Fungi|p__Basidiomycota|c__Tremellomycetes|o__Cystofilobasidiales|f__Mrakiaceae|g__Udeniomyces|s__Udeniomyces pyricola",2759|4751|1913637|2212703|4827|34489|64644;2759|4751|1913637|2212703|4827|34489|64644|64647;2759|4751|4890|147545|5042|1131492|5052|41959;2759|4751|4890|147545|5042|1131492|5052|46472;2759|4751|4890|147541|451869|45131|45132;2759|4751|4890|3239874|2916678|766764|5475;2759|4751|4890|3239874|2916678|766764|5475|5476;2759|4751|4890|3239873|3243772|34353|27314;2759|4751|4890|3239873|3243772|34353|27316;2759|4751|4890|3239873|3243772|34353|43987|1206149;2759|4751|4890|3239873|3243772|34353|43987|1173061;2759|4751|5204|1538075|162474|742845|55193;2759|4751|1913637|2212703|4827|34489|4830;2759|4751|1913637|2212703|4827|34489|4830|36080;2759|4751|1913637|2212703|4827|34489|4830|2021227;2759|4751|5204|162481|231213|1799696|5533;2759|4751|5204|162481|231213|1799696|5533|5537;2759|4751|4890|147545|5042|28568|5094|1400007;2759|4751|5204|155616|90883|1851551|42658;2759|4751|5204|155616|90883|1851551|42658|42659;2759|4751|5204|155616|90883|1851551|42658|42661,Complete,Svetlana up @@ -6015,13 +6015,13 @@ bsdb:1086/8/2,Study 1086,case-control,38745393,10.1111/jcpe.13998,NA,"Bingöl M, bsdb:1086/9/1,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 9,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Saliva (Ctrl-S) patients,Control Subgingival plaque (Ctrl-SP) patients,Healthy Controls who stimulated Subgingival plaque samples were gotten from.,114,113,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Appendix Table 10,12 August 2024,MyleeeA,"MyleeeA,Tosin",Differential abundant genera in Control Saliva (Ctrl-S) and Control Subgingival Plague (Ctrl-SP) patients,increased,"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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum",2|3379134|976|200643|171549|171552|1283313;2|1783272|201174|84998|84999|1643824|1380;2|1783272|1239|91061|1385|539738|1378;2|3379134|1224|1236|135625|712|724;2|3379134|1224|28216|206351|481|482;2|1783272|1239|186801|3085636|186803|265975;2|1783272|1239|186801|3082720|186804|1257;2|3379134|976|200643|171549|171551|836;2|3379134|976|200643|171549|171552|838;2|1783272|1239|186801|3085636|186803|1213720;2|1783272|1239|91061|186826|1300|1301;2|1783272|1239|909932|1843489|31977|29465;2759|33090|35493|3398|72025|3803|3814|508215;2|1783272|1239|186801|3085636|186803|1164882,Complete,NA bsdb:1086/9/2,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 9,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Saliva (Ctrl-S) patients,Control Subgingival plaque (Ctrl-SP) patients,Healthy Controls who stimulated Subgingival plaque samples were gotten from.,114,113,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Appendix Table 10,12 August 2024,MyleeeA,"MyleeeA,Tosin",Differential abundant genera in Control Saliva (Ctrl-S) and Control Subgingival plague (Ctrl-SP) patients,decreased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Leptotrichiaceae|g__Leptotrichia,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",2|3379134|1224|1236|135625|712|416916;2|1783272|201174|1760|85009|31957|2801844;2|3379134|29547|3031852|213849|72294|194;2|3379134|976|117743|200644|49546|1016;2|3379134|1224|1236|135615|868|2717;2|1783272|201174|1760|85007|1653|1716;2|3384189|32066|203490|203491|203492|848;2|3379134|1224|28216|206351|481|32257;2|3384189|32066|203490|203491|1129771|32067;2|1783272|201174|84998|84999|1643824|133925;2|1783272|1239|909932|909929|1843491|970;2|3379134|976|200643|171549|2005525|195950,Complete,NA bsdb:1086/10/1,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 10,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Adults Saliva (Ctrl-Adults-S) patients,Control Adults Subgingival plaque (Ctrl-Adults-SP) patients,Healthy Control adults who stimulated Sub gingival plaque samples were gotten from,52,52,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Appendix Table 10,12 August 2024,MyleeeA,"MyleeeA,Tosin",Differential abundant genera in Control Adults Saliva (Ctrl-Adults-S) and Control Adults Subgingival plague (Ctrl-Adults-SP) patients,increased,"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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|3379134|976|200643|171549|171552|1283313;2|1783272|201174|84998|84999|1643824|1380;2|1783272|1239|91061|1385|539738|1378;2|3379134|1224|1236|135625|712|724;2|3379134|1224|28216|206351|481|482;2|1783272|1239|186801|3085636|186803|265975;2|1783272|1239|186801|3082720|186804|1257;2|3379134|976|200643|171549|171551|836;2|3379134|976|200643|171549|171552|838;2|1783272|1239|186801|3085636|186803|1213720;2|1783272|1239|91061|186826|1300|1301;2|1783272|1239|909932|1843489|31977|29465;2759|33090|35493|3398|72025|3803|3814|508215,Complete,NA -bsdb:1086/10/2,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 10,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Adults Saliva (Ctrl-Adults-S) patients,Control Adults Subgingival plaque (Ctrl-Adults-SP) patients,Healthy Control adults who stimulated Sub gingival plaque samples were gotten from,52,52,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Appendix Table 10,12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva (Ctrl-S) and Control Subgingival plague (Ctrl-SP) patients.,decreased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,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__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",2|3379134|1224|1236|135625|712|416916;2|1783272|201174|1760|85009|31957|2801844;2|3379134|29547|3031852|213849|72294|194;2|3379134|976|117743|200644|49546|1016;2|3379134|1224|1236|135615|868|2717;2|1783272|201174|1760|85007|1653|1716;2|3384189|32066|203490|203491|203492|848;2|3379134|1224|28216|206351|481|32257;2|1783272|201174|84998|84999|1643824|133925;2|1783272|1239|909932|909929|1843491|970;2|3379134|976|200643|171549|2005525|195950,Complete,NA -bsdb:1086/11/1,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 11,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Children (CTRL Ch-S),Control Children (CTRL Ch-SP),Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.,62,61,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva and Control Subgingival plague Children samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|838;2|1239|186801|3085636|186803|265975;2|976|200643|171549|171551|836;2|1224|28216|206351|481|482;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3082720|186804|1257;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA -bsdb:1086/11/2,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 11,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Children (CTRL Ch-S),Control Children (CTRL Ch-SP),Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.,62,61,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in Control Saliva and Control Subgingival plague Children samples,decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium",2|976|117743|200644|49546|1016;2|32066|203490|203491|203492|848;2|201174|1760|85007|1653|1716;2|1224|28216|206351|481|32257;2|201174|1760|85009|31957|2801844;2|1224|1236|135615|868|2717;2|201174|84998|84999|1643824|133925;2|976|200643|171549|2005525|195950;2|29547|3031852|213849|72294|194;2|508458|649775|649776|3029087|1434006,Complete,NA -bsdb:1086/12/1,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 12,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria (PKU-S),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,109,96,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Patient samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1224|28216|206351|481|482;2|1239|186801|3085636|186803|265975;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA -bsdb:1086/12/2,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 12,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria (PKU-S),Phenylketonuria (PKU-SP),Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,109,96,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Patients samples,decreased,"k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|201174|1760|2037|2049|1654;2|1224|1236|135625|712|416916;2|201174|1760|85009|31957|2801844;2|29547|3031852|213849|72294|194;2|976|117743|200644|49546|1016;2|1224|1236|135615|868|2717;2|201174|1760|85007|1653|1716;2|508458|649775|649776|3029087|1434006;2|32066|203490|203491|203492|848;2|1224|28216|206351|481|32257;2|1224|28216|80840|119060|47670;2|201174|84998|84999|1643824|133925;2|1239|186801|186802|186807|2740;2|1239|909932|909929|1843491|970;2|976|200643|171549|2005525|195950,Complete,NA -bsdb:1086/13/1,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 13,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Adults (PKU-S),Phenylketonuria Adults (PKU-SP),Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,50,45,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|3085636|186803|1164882;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA -bsdb:1086/13/2,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 13,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Adults (PKU-S),Phenylketonuria Adults (PKU-SP),Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,50,45,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|29547|3031852|213849|72294|194;2|1239|186801|186802|186807|2740;2|201174|84998|84999|1643824|133925;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|1654;2|1239|909932|909929|1843491|970;2|201174|1760|85009|31957|2801844;2|508458|649775|649776|3029087|1434006;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|976|117743|200644|49546|1016,Complete,NA +bsdb:1086/10/2,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 10,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Adults Saliva (Ctrl-Adults-S) patients,Control Adults Subgingival plaque (Ctrl-Adults-SP) patients,Healthy Control adults who stimulated Sub gingival plaque samples were gotten from,52,52,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Appendix Table 10,12 August 2024,MyleeeA,"MyleeeA,Tosin",Differential abundant genera in Control Adults Saliva (Ctrl-Adults-S) and Control Adults Subgingival plague (Ctrl-Adults-SP) patients.,decreased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter,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__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella",2|3379134|1224|1236|135625|712|416916;2|1783272|201174|1760|85009|31957|2801844;2|3379134|29547|3031852|213849|72294|194;2|3379134|976|117743|200644|49546|1016;2|3379134|1224|1236|135615|868|2717;2|1783272|201174|1760|85007|1653|1716;2|3384189|32066|203490|203491|203492|848;2|1783272|1239|909932|909929|1843491|970;2|3379134|976|200643|171549|2005525|195950,Complete,NA +bsdb:1086/11/1,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 11,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Children Saliva (Ctrl-Ch-S) patients,Control Children Subgingival plaque (Ctrl-Ch-SP) patients,Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.,62,61,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Appendix Table 10,12 August 2024,MyleeeA,"MyleeeA,Tosin",Differential abundant genera in Control Children Saliva (Ctrl-Ch-S) and Control children Subgingival plague (Ctrl-Ch-SP) patients.,increased,"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__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,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__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia",2|3379134|976|200643|171549|171552|1283313;2|1783272|201174|84998|84999|1643824|1380;2|1783272|1239|91061|1385|539738|1378;2|3379134|1224|1236|135625|712|724;2|3379134|1224|28216|206351|481|482;2|1783272|1239|186801|3085636|186803|265975;2|1783272|1239|186801|3082720|186804|1257;2|3379134|976|200643|171549|171551|836;2|3379134|976|200643|171549|171552|838;2|1783272|1239|186801|3085636|186803|1213720;2|1783272|1239|91061|186826|1300|1301;2|1783272|1239|909932|1843489|31977|29465;2759|33090|35493|3398|72025|3803|3814|508215,Complete,NA +bsdb:1086/11/2,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 11,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Control Children Saliva (Ctrl-Ch-S) patients,Control Children Subgingival plaque (Ctrl-Ch-SP) patients,Healthy Control Children without PKU who stimulated Sub gingival plaque samples were gotten from.,62,61,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Appendix Table 10,12 August 2024,MyleeeA,"MyleeeA,Tosin",Differential abundant genera in Control Children Saliva (Ctrl-Ch-S) and Control children Subgingival plague (Ctrl-Ch-SP) patients.,decreased,"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__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Aggregatibacter",2|1783272|201174|1760|85009|31957|2801844;2|3379134|29547|3031852|213849|72294|194;2|3379134|976|117743|200644|49546|1016;2|3379134|1224|1236|135615|868|2717;2|1783272|201174|1760|85007|1653|1716;2|3384189|32066|203490|203491|203492|848;2|3379134|976|200643|171549|2005525|195950;2|1783272|1239|909932|909929|1843491|970;2|3379134|1224|1236|135625|712|416916,Complete,NA +bsdb:1086/12/1,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 12,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Saliva (PKU-S) patients,Phenylketonuria Subgingival plaque (PKU-SP) patients,Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,109,96,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Appendix Table 10,12 August 2024,MyleeeA,"MyleeeA,Tosin",Differential abundant genera in PKU Saliva (PKU-S) and PKU Subgingival plague (PKU-SP) Patient s,increased,"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__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Oribacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,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__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,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",2|3379134|976|200643|171549|171552|1283313;2|1783272|201174|84998|84999|1643824|1380;2|1783272|1239|91061|1385|539738|1378;2|3379134|1224|1236|135625|712|724;2|1783272|1239|186801|3085636|186803|1164882;2|3379134|1224|28216|206351|481|482;2|1783272|1239|186801|3085636|186803|265975;2|1783272|1239|186801|3082720|186804|1257;2|3379134|976|200643|171549|171551|836;2|3379134|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1783272|1239|186801|3085636|186803|1213720;2|1783272|1239|91061|186826|1300|1301;2|1783272|1239|909932|1843489|31977|29465,Complete,NA +bsdb:1086/12/2,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 12,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Saliva (PKU-S) patients,Phenylketonuria Subgingival plaque (PKU-SP) patients,Patients diagnosed with Phenylketonuria (PKU) and who stimulated Sub gingival plaque samples were gotten from.,109,96,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Appendix Table 10,12 August 2024,MyleeeA,"MyleeeA,Tosin",Differneti abundant genera in PKU Saliva (PKU-S) and PKU Subgingival plague (PKU-SP) Patients.,decreased,"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__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,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,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella",2|1783272|201174|1760|2037|2049|1654;2|1783272|201174|1760|85009|31957|2801844;2|3379134|29547|3031852|213849|72294|194;2|3379134|976|117743|200644|49546|1016;2|3379134|1224|1236|135615|868|2717;2|1783272|201174|1760|85007|1653|1716;2|3384194|508458|649775|649776|3029087|1434006;2|3384189|32066|203490|203491|203492|848;2|3379134|1224|28216|206351|481|32257;2|1783272|1239|186801|186802|186807|2740;2|1783272|1239|909932|909929|1843491|970;2|3379134|976|200643|171549|2005525|195950;2|1783272|201174|84998|84999|1643824|133925,Complete,NA +bsdb:1086/13/1,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 13,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Adults Saliva (PKU-Adults-S),Phenylketonuria Adults Subgingival plaque (PKU-Adults-SP),Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,50,45,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Stomatobaculum,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|838;2759|33090|35493|3398|72025|3803|3814|508215;2|1239|186801|3085636|186803|1164882;2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1213720;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA +bsdb:1086/13/2,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 13,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Adults Saliva (PKU-Adults-S),Phenylketonuria Adults Subgingival plaque (PKU-Adults-SP),Adult Patients diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,50,45,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga",2|29547|3031852|213849|72294|194;2|1239|186801|186802|186807|2740;2|201174|84998|84999|1643824|133925;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|1654;2|1239|909932|909929|1843491|970;2|201174|1760|85009|31957|2801844;2|508458|649775|649776|3029087|1434006;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|976|117743|200644|49546|1016,Complete,NA bsdb:1086/14/1,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 14,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Ch (PKU-S),Phenylketonuria Ch (PKU-SP),Children diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,59,51,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 1,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Children samples,increased,"k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Alloprevotella,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus,k__Bacteria|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Porphyromonas,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus,k__Bacteria|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella",2|976|200643|171549|171552|1283313;2|201174|84998|84999|1643824|1380;2|1239|91061|1385|539738|1378;2|1224|1236|135625|712|724;2|1239|186801|3085636|186803|1164882;2|1224|28216|206351|481|482;2|1239|186801|3082720|186804|1257;2|976|200643|171549|171551|836;2|976|200643|171549|171552|838;2|1239|91061|186826|1300|1301;2|1239|909932|1843489|31977|29465,Complete,NA bsdb:1086/14/2,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 14,Germany,Homo sapiens,Mouth,UBERON:0000165,Phenylketonuria,MONDO:0009861,Phenylketonuria Ch (PKU-S),Phenylketonuria Ch (PKU-SP),Children diagnosed with Phenylketonuria (PKU) and who stimulated Subgingival plaque samples were gotten from.,59,51,NA,16S,12,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,age,NA,NA,NA,NA,NA,NA,NA,Signature 2,Figure 2(D),12 August 2024,MyleeeA,MyleeeA,Differential abundant genera in PKU Saliva and PKU Subgingival plague Adult samples,decreased,"k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter,k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Tannerella,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Peptococcaceae|g__Peptococcus,k__Bacteria|p__Actinomycetota|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Cardiobacteriales|f__Cardiobacteriaceae|g__Cardiobacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces,k__Bacteria|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Selenomonas,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Aminobacteriaceae|g__Fretibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia",2|29547|3031852|213849|72294|194;2|976|200643|171549|2005525|195950;2|1239|186801|186802|186807|2740;2|201174|84998|84999|1643824|133925;2|1224|1236|135615|868|2717;2|201174|1760|2037|2049|1654;2|1239|909932|909929|1843491|970;2|1224|28216|206351|481|32257;2|508458|649775|649776|3029087|1434006;2|201174|1760|85007|1653|1716;2|32066|203490|203491|203492|848;2|976|117743|200644|49546|1016;2|201174|1760|85009|31957|2801844,Complete,NA 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 @@ -6576,7 +6576,7 @@ bsdb:1163/3/2,Study 1163,"cross-sectional observational, not case-control",28362 bsdb:1163/4/1,Study 1163,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán MJ, Pérez-Matute P, Recio-Fernández E, Lezana Rosales JM , Oteo JA",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (C0ntrol),NRTIs + NNRTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs),21,22,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 2,9 January 2025,Joiejoie,Joiejoie,Relative abundance of major phyla present in the gut in NRTIs + NNRTIs.,increased,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota,2|3379134|1224,Complete,NA bsdb:1163/4/2,Study 1163,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán MJ, Pérez-Matute P, Recio-Fernández E, Lezana Rosales JM , Oteo JA",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 4,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (C0ntrol),NRTIs + NNRTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs),21,22,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 2,Table 2,9 January 2025,Joiejoie,Joiejoie,Relative abundance of major phyla present in the gut in NRTIs + NNRTIs.,decreased,NA,NA,Complete,NA bsdb:1163/5/1,Study 1163,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán MJ, Pérez-Matute P, Recio-Fernández E, Lezana Rosales JM , Oteo JA",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Non-infected volunteers (Control),NRTIs + INSTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) with integrase strand transfer inhibitors (INSTIs),21,8,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 2,9 January 2025,NA,NA,Relative abundance of major phyla present in the gut in NRTIs + INSTIs.,increased,NA,NA,Complete,NA -bsdb:1163/5/2,Study 1163,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán MJ, Pérez-Matute P, Recio-Fernández E, Lezana Rosales JM , Oteo JA",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Non-infected volunteers (Control),NRTIs + INSTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) with integrase strand transfer inhibitors (INSTIs),21,8,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 2,Table 2,9 January 2025,NA,NA,Relative abundance of major phyla present in the gut in NRTIs + INSTIs.,decreased,NA,NA,Complete,NA +bsdb:1163/5/2,Study 1163,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán MJ, Pérez-Matute P, Recio-Fernández E, Lezana Rosales JM , Oteo JA",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 5,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,Non-infected volunteers (Control),NRTIs + INSTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) with integrase strand transfer inhibitors (INSTIs),21,8,3 months,16S,4,Illumina,Kruskall-Wallis,0.05,TRUE,NA,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 2,Table 2,9 January 2025,Joiejoie,Joiejoie,Relative abundance of major phyla present in the gut in NRTIs + INSTIs.,decreased,k__Bacteria|k__Bacillati|p__Bacillota,2|1783272|1239,Complete,NA bsdb:1163/6/1,Study 1163,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán MJ, Pérez-Matute P, Recio-Fernández E, Lezana Rosales JM , Oteo JA",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs+PIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs),21,15,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 1,Table 3,9 January 2025,NA,NA,"Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+PIs",increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|s__Clostridiales bacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,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__Flavonifractor|s__Flavonifractor plautii",2|1783272|1239|186801|186802|1898207;2|1783272|1239|186801|3085636|186803;2|1783272|201174|84998|1643822|1643826|84111;2|1783272|1239|186801|186802|216572|946234|292800,Complete,NA bsdb:1163/6/2,Study 1163,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán MJ, Pérez-Matute P, Recio-Fernández E, Lezana Rosales JM , Oteo JA",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 6,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs+PIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs),21,15,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,decreased,decreased,NA,NA,decreased,Signature 2,Table 3,9 January 2025,NA,NA,"Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+PIs",decreased,"k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Solobacterium",2|1783272|201174|1760|2037;2|3379134|1224|1236|72274;2|3379134|1224|28211|204457;2|3379134|976|200643|171549|171552;2|3379134|976|200643|171549|171552|838;2|1783272|1239|526524|526525|128827|123375,Complete,NA bsdb:1163/7/1,Study 1163,"cross-sectional observational, not case-control",28362071,https://doi.org/10.7448/IAS.20.1.21526,NA,"Villanueva-Millán MJ, Pérez-Matute P, Recio-Fernández E, Lezana Rosales JM , Oteo JA",Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients,Journal of the International AIDS Society,2017,"HIV infection, antiretroviral therapy, bacterial diversity, gut microbiota, inflammation, microbial translocation",Experiment 7,Spain,Homo sapiens,Feces,UBERON:0001988,HIV infection,EFO:0000764,non-infected volunteers (Control),NRTIs + NNRTIs,This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs),21,22,3 months,16S,4,Illumina,Mann-Whitney (Wilcoxon),0.05,TRUE,NA,"age,body mass index,sex",NA,NA,increased,increased,NA,NA,increased,Signature 1,Table 3,9 January 2025,NA,NA,"Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+NNRTIs",increased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes senegalensis,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|s__Bacteroidaceae bacterium,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|s__Bacteroidales bacterium,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,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus",2|3379134|976|200643|171549|171550|239759|1288121;2|3379134|976|200643|171549|815|2212467;2|3379134|976|200643|171549|2030927;2|1783272|201174|84998|84999|84107;2|1783272|201174|84998|84999;2|1783272|1239|186801|3085636|186803;2|3379134|1224|1236|72274|135621|286;2|1783272|1239|91061|186826|1300|1301,Complete,NA