diff --git a/bugsigdb_signatures_genus_metaphlan.gmt b/bugsigdb_signatures_genus_metaphlan.gmt index 05207a58f..735bfa5cd 100644 --- a/bugsigdb_signatures_genus_metaphlan.gmt +++ b/bugsigdb_signatures_genus_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -5555,3 +5555,11 @@ bsdb:1283/3/1_Response-to-diet:Effective-group-after-the-therapy-(Y2)_vs_Effecti bsdb:1284/1/2_Hyperglycemia:Hyperglycemic-group_vs_Normoglycemic-group_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1284/2/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Curtobacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium bsdb:1284/2/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia diff --git a/bugsigdb_signatures_genus_metaphlan_exact.gmt b/bugsigdb_signatures_genus_metaphlan_exact.gmt index 317493aa6..94db6800d 100644 --- a/bugsigdb_signatures_genus_metaphlan_exact.gmt +++ b/bugsigdb_signatures_genus_metaphlan_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -4785,3 +4785,11 @@ bsdb:1283/3/1_Response-to-diet:Effective-group-after-the-therapy-(Y2)_vs_Effecti bsdb:1284/1/2_Hyperglycemia:Hyperglycemic-group_vs_Normoglycemic-group_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides bsdb:1284/2/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Acinetobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Sphingomonadales|f__Sphingomonadaceae|g__Sphingomonas k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Burkholderia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae|g__Pseudonocardia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Lachnoanaerobaculum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Bacillales|g__Exiguobacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria|o__Hyphomicrobiales|f__Brucellaceae|g__Ochrobactrum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Proteus k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Morganellaceae|g__Providencia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Sphaerotilaceae|g__Roseateles k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Curtobacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Veillonella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Aeromonadaceae|g__Aeromonas k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Gordoniaceae|g__Gordonia k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Microbacteriaceae|g__Microbacterium bsdb:1284/2/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Megasphaera k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Faecalibacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Romboutsia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia diff --git a/bugsigdb_signatures_genus_ncbi.gmt b/bugsigdb_signatures_genus_ncbi.gmt index 7a26caca2..dc8533f5b 100644 --- a/bugsigdb_signatures_genus_ncbi.gmt +++ b/bugsigdb_signatures_genus_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -5555,3 +5555,11 @@ bsdb:1283/3/1_Response-to-diet:Effective-group-after-the-therapy-(Y2)_vs_Effecti bsdb:1284/1/2_Hyperglycemia:Hyperglycemic-group_vs_Normoglycemic-group_DOWN NA 1357 1164882 2053 816 bsdb:1284/2/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA 613 40323 469 13687 1378 1386 1716 32008 482 838 1847 1164882 1301 848 33986 528 583 586 93681 32207 2034 724 194 1357 29465 642 2053 33882 bsdb:1284/2/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA 906 216851 572511 816 1263 1501226 1485 1678 570 +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 572511 1730 1257 1263 44748 292632 46123 +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 724 158846 841 +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 1730 1257 44748 292632 1263 46123 +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 1263 46123 +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA 1730 1257 44748 292632 1263 46123 +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA 572511 diff --git a/bugsigdb_signatures_genus_ncbi_exact.gmt b/bugsigdb_signatures_genus_ncbi_exact.gmt index 4fda78a77..8d45aa5e8 100644 --- a/bugsigdb_signatures_genus_ncbi_exact.gmt +++ b/bugsigdb_signatures_genus_ncbi_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -4785,3 +4785,11 @@ bsdb:1283/3/1_Response-to-diet:Effective-group-after-the-therapy-(Y2)_vs_Effecti bsdb:1284/1/2_Hyperglycemia:Hyperglycemic-group_vs_Normoglycemic-group_DOWN NA 1357 1164882 2053 816 bsdb:1284/2/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA 613 40323 469 13687 1378 1386 1716 32008 482 838 1847 1164882 1301 848 33986 528 583 586 93681 32207 2034 724 194 1357 29465 642 2053 33882 bsdb:1284/2/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA 906 216851 572511 816 1263 1501226 1485 1678 570 +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 572511 1730 1257 1263 44748 292632 46123 +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 724 158846 841 +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 1730 1257 44748 292632 1263 46123 +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 1263 46123 +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA 1730 1257 44748 292632 1263 46123 +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA 572511 diff --git a/bugsigdb_signatures_genus_taxname.gmt b/bugsigdb_signatures_genus_taxname.gmt index 8ed7bf5c4..7ab098829 100644 --- a/bugsigdb_signatures_genus_taxname.gmt +++ b/bugsigdb_signatures_genus_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -5555,3 +5555,11 @@ bsdb:1283/3/1_Response-to-diet:Effective-group-after-the-therapy-(Y2)_vs_Effecti bsdb:1284/1/2_Hyperglycemia:Hyperglycemic-group_vs_Normoglycemic-group_DOWN NA Lactococcus Lachnoanaerobaculum Gordonia Bacteroides bsdb:1284/2/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA Serratia Stenotrophomonas Acinetobacter Sphingomonas Gemella Bacillus Corynebacterium Burkholderia Neisseria Prevotella Pseudonocardia Lachnoanaerobaculum Streptococcus Fusobacterium Exiguobacterium Ochrobactrum Proteus Providencia Roseateles Rothia Curtobacterium Haemophilus Campylobacter Lactococcus Veillonella Aeromonas Gordonia Microbacterium bsdb:1284/2/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA Megasphaera Faecalibacterium Blautia Bacteroides Ruminococcus Romboutsia Clostridium Bifidobacterium Klebsiella +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Blautia Eubacterium Peptostreptococcus Ruminococcus Sporobacter Subdoligranulum Abiotrophia +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia Haemophilus Megamonas Roseburia +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Eubacterium Peptostreptococcus Sporobacter Subdoligranulum Ruminococcus Abiotrophia +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Ruminococcus Abiotrophia +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA Eubacterium Peptostreptococcus Sporobacter Subdoligranulum Ruminococcus Abiotrophia +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA Blautia diff --git a/bugsigdb_signatures_genus_taxname_exact.gmt b/bugsigdb_signatures_genus_taxname_exact.gmt index 8a3fd6c30..cb7490612 100644 --- a/bugsigdb_signatures_genus_taxname_exact.gmt +++ b/bugsigdb_signatures_genus_taxname_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -4785,3 +4785,11 @@ bsdb:1283/3/1_Response-to-diet:Effective-group-after-the-therapy-(Y2)_vs_Effecti bsdb:1284/1/2_Hyperglycemia:Hyperglycemic-group_vs_Normoglycemic-group_DOWN NA Lactococcus Lachnoanaerobaculum Gordonia Bacteroides bsdb:1284/2/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA Serratia Stenotrophomonas Acinetobacter Sphingomonas Gemella Bacillus Corynebacterium Burkholderia Neisseria Prevotella Pseudonocardia Lachnoanaerobaculum Streptococcus Fusobacterium Exiguobacterium Ochrobactrum Proteus Providencia Roseateles Rothia Curtobacterium Haemophilus Campylobacter Lactococcus Veillonella Aeromonas Gordonia Microbacterium bsdb:1284/2/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA Megasphaera Faecalibacterium Blautia Bacteroides Ruminococcus Romboutsia Clostridium Bifidobacterium Klebsiella +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Blautia Eubacterium Peptostreptococcus Ruminococcus Sporobacter Subdoligranulum Abiotrophia +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia Haemophilus Megamonas Roseburia +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Eubacterium Peptostreptococcus Sporobacter Subdoligranulum Ruminococcus Abiotrophia +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Ruminococcus Abiotrophia +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA Eubacterium Peptostreptococcus Sporobacter Subdoligranulum Ruminococcus Abiotrophia +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA Blautia diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt index 4ecfc2e05..c166caef9 100644 --- a/bugsigdb_signatures_mixed_metaphlan.gmt +++ b/bugsigdb_signatures_mixed_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -6773,3 +6773,15 @@ bsdb:1284/3/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA k__Bacteria|k_ bsdb:1284/3/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales k__Bacteria|k__Bacillati|p__Bacillota k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia k__Bacteria|k__Pseudomonadati|p__Bacteroidota k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae bsdb:1284/4/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota k__Bacteria|k__Bacillati|p__Actinomycetota k__Bacteria|k__Fusobacteriati|p__Fusobacteriota k__Bacteria|k__Bacillati|p__Actinomycetota|c__Acidimicrobiia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae bsdb:1284/4/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota k__Bacteria|k__Bacillati|p__Bacillota k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales 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 k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota +bsdb:1285/2/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria +bsdb:1285/2/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota +bsdb:1285/3/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota +bsdb:1285/3/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt index 0374c9716..679249a5e 100644 --- a/bugsigdb_signatures_mixed_ncbi.gmt +++ b/bugsigdb_signatures_mixed_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -6773,3 +6773,15 @@ bsdb:1284/3/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA 1224 201174 32 bsdb:1284/3/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA 135624 1239 171549 200643 976 186801 526524 186802 186803 216572 171552 83763 bsdb:1284/4/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA 1224 201174 32066 84992 28211 91061 3031852 203490 1236 909932 135625 909929 72274 186826 91347 85006 119060 712 31977 135621 186828 481 bsdb:1284/4/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA 976 1239 200643 186801 526524 171549 135624 186802 171552 83763 186803 216572 +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 572511 186802 1730 186803 1257 216572 1263 44748 292632 46123 28216 +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 186802 724 186803 158846 841 203494 74201 +bsdb:1285/2/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 28216 +bsdb:1285/2/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 203494 74201 +bsdb:1285/3/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA 203494 74201 +bsdb:1285/3/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA 28216 +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 186803 1730 1257 44748 292632 1263 46123 +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA 816 186803 1263 46123 +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA 816 572511 +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA 1730 186803 1257 44748 292632 1263 46123 +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA 572511 diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt index 6a86de1f5..d9a071261 100644 --- a/bugsigdb_signatures_mixed_taxname.gmt +++ b/bugsigdb_signatures_mixed_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_08:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -6773,3 +6773,15 @@ bsdb:1284/3/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA Pseudomonadota bsdb:1284/3/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA Aeromonadales Bacillota Bacteroidales Bacteroidia Bacteroidota Clostridia Erysipelotrichia Eubacteriales Lachnospiraceae Oscillospiraceae Prevotellaceae Succinivibrionaceae bsdb:1284/4/1_Sampling-site:Biopsy-samples_vs_Stool-samples_UP NA Pseudomonadota Actinomycetota Fusobacteriota Acidimicrobiia Alphaproteobacteria Bacilli Epsilonproteobacteria Fusobacteriia Gammaproteobacteria Negativicutes Pasteurellales Selenomonadales Pseudomonadales Lactobacillales Enterobacterales Micrococcales Burkholderiaceae Pasteurellaceae Veillonellaceae Pseudomonadaceae Carnobacteriaceae Neisseriaceae bsdb:1284/4/2_Sampling-site:Biopsy-samples_vs_Stool-samples_DOWN NA Bacteroidota Bacillota Bacteroidia Clostridia Erysipelotrichia Bacteroidales Aeromonadales Eubacteriales Prevotellaceae Succinivibrionaceae Lachnospiraceae Oscillospiraceae +bsdb:1285/1/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Blautia Eubacteriales Eubacterium Lachnospiraceae Peptostreptococcus Oscillospiraceae Ruminococcus Sporobacter Subdoligranulum Abiotrophia Betaproteobacteria +bsdb:1285/1/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia Eubacteriales Haemophilus Lachnospiraceae Megamonas Roseburia Verrucomicrobiia Verrucomicrobiota +bsdb:1285/2/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Betaproteobacteria +bsdb:1285/2/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Verrucomicrobiia Verrucomicrobiota +bsdb:1285/3/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA Verrucomicrobiia Verrucomicrobiota +bsdb:1285/3/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA Betaproteobacteria +bsdb:1285/4/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Lachnospiraceae Eubacterium Peptostreptococcus Sporobacter Subdoligranulum Ruminococcus Abiotrophia +bsdb:1285/4/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia +bsdb:1285/5/1_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_UP NA Bacteroides Lachnospiraceae Ruminococcus Abiotrophia +bsdb:1285/5/2_Prediabetes-syndrome:Prediabetes-(Pre-DM)_vs_Normal-Glucose-Tolerance-(NGT)_DOWN NA Bacteroides Blautia +bsdb:1285/6/1_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_UP NA Eubacterium Lachnospiraceae Peptostreptococcus Sporobacter Subdoligranulum Ruminococcus Abiotrophia +bsdb:1285/6/2_Diabetes-mellitus:Type-2-diabetes-mellitus-(T2DM)_vs_Prediabetes-(Pre-DM)_DOWN NA Blautia diff --git a/file_size.csv b/file_size.csv index d4a91967f..574d6d118 100644 --- a/file_size.csv +++ b/file_size.csv @@ -3105,3 +3105,4 @@ "2025-02-07_08:58_UTC" "4787" "5557" "4787" "5557" "4787" "5557" "6775" "6775" "6775" "3086" "3086" "3086" "3086" "3086" "3086" "4355" "7726" "7316" "1391" "2025-02-07_09:58_UTC" "4787" "5557" "4787" "5557" "4787" "5557" "6775" "6775" "6775" "3086" "3086" "3086" "3086" "3086" "3086" "4355" "7726" "7316" "1392" "2025-02-07_10:58_UTC" "4787" "5557" "4787" "5557" "4787" "5557" "6775" "6775" "6775" "3086" "3086" "3086" "3086" "3086" "3086" "4362" "7727" "7316" "1393" +"2025-02-07_11:58_UTC" "4795" "5565" "4795" "5565" "4795" "5565" "6787" "6787" "6787" "3086" "3086" "3086" "3086" "3086" "3086" "4362" "7739" "7328" "1394" diff --git a/full_dump.csv b/full_dump.csv index 085301617..cfd77c6d6 100644 --- a/full_dump.csv +++ b/full_dump.csv @@ -1,4 +1,4 @@ -# BugSigDB 2025-02-07_10:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-02-07_11:58_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 @@ -7724,4 +7724,16 @@ bsdb:1284/3/1,Study 1284,"cross-sectional observational, not case-control",NA,ht bsdb:1284/3/2,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 3,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from participants with hyperglycemia.,33,33,6–8 weeks,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1,7 February 2025,Aleru Divine,Aleru Divine,"Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.",decreased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|k__Bacillati|p__Bacillota,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacteria|k__Pseudomonadati|p__Bacteroidota,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae",2|3379134|1224|1236|135624;2|1783272|1239;2|3379134|976|200643|171549;2|3379134|976|200643;2|3379134|976;2|1783272|1239|186801;2|1783272|1239|526524;2|1783272|1239|186801|186802;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572;2|3379134|976|200643|171549|171552;2|3379134|1224|1236|135624|83763,Complete,NA bsdb:1284/4/1,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 4,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from normoglycemic participants.,33,33,6–8 weeks,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 1,Supplementary Figure 1,7 February 2025,NA,NA,"Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.",increased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota,k__Bacteria|k__Bacillati|p__Actinomycetota,k__Bacteria|k__Fusobacteriati|p__Fusobacteriota,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Acidimicrobiia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Alphaproteobacteria,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli,k__Bacteria|k__Pseudomonadati|p__Campylobacterota|c__Epsilonproteobacteria,k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Micrococcales,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Veillonellales|f__Veillonellaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae",2|3379134|1224;2|1783272|201174;2|3384189|32066;2|1783272|201174|84992;2|3379134|1224|28211;2|1783272|1239|91061;2|3379134|29547|3031852;2|3384189|32066|203490;2|3379134|1224|1236;2|1783272|1239|909932;2|3379134|1224|1236|135625;2|1783272|1239|909932|909929;2|3379134|1224|1236|72274;2|1783272|1239|91061|186826;2|3379134|1224|1236|91347;2|1783272|201174|1760|85006;2|3379134|1224|28216|80840|119060;2|3379134|1224|1236|135625|712;2|1783272|1239|909932|1843489|31977;2|3379134|1224|1236|72274|135621;2|1783272|1239|91061|186826|186828;2|3379134|1224|28216|206351|481,Complete,NA bsdb:1284/4/2,Study 1284,"cross-sectional observational, not case-control",NA,https://doi.org/10.1038/s41598-023-37720-x,NA,"Aarti Darra, Anish Bhattacharya, Anupam Kumar Singh, Anuraag Jena, Anurag Agrawal, Pankaj Gupta, Priyanka Popli, Ritambhra Nada, Sanjay Kumar Bhadada, Usha Dutta, Vandana Singh, Vishal Sharma",Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment,Scientific reports,2023,NA,Experiment 4,India,Homo sapiens,"Feces,Duodenum","UBERON:0001988,UBERON:0002114",Sampling site,EFO:0000688,Stool samples,Biopsy samples,Duodenal biopsy samples from normoglycemic participants.,33,33,6–8 weeks,16S,34,Illumina,DESeq2,0.05,TRUE,NA,NA,age,NA,NA,NA,NA,NA,NA,Signature 2,Supplementary Figure 1,7 February 2025,NA,NA,"Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.",decreased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota,k__Bacteria|k__Bacillati|p__Bacillota,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia,k__Bacteria|k__Bacillati|p__Bacillota|c__Erysipelotrichia,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Aeromonadales|f__Succinivibrionaceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae",2|3379134|976;2|1783272|1239;2|3379134|976|200643;2|1783272|1239|186801;2|1783272|1239|526524;2|3379134|976|200643|171549;2|3379134|1224|1236|135624;2|1783272|1239|186801|186802;2|3379134|976|200643|171549|171552;2|3379134|1224|1236|135624|83763;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572,Complete,NA +bsdb:1285/1/1,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Normal Glucose Tolerance (NGT),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,44,13,1 month,16S,345,Roche454,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,"Table 2, Table S3 and Table S4",7 February 2025,NA,NA,The relative abundance of OTUs enriched in the NGT and T2DM groups.,increased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria",2|3379134|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|186802;2|1783272|1239|186801|186802|186806|1730;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|3082720|186804|1257;2|1783272|1239|186801|186802|216572;2|1783272|1239|186801|186802|216572|1263;2|1783272|1239|186801|186802|216572|44748;2|1783272|1239|186801|186802|216572|292632;2|1783272|1239|91061|186826|186827|46123;2|3379134|1224|28216,Complete,NA +bsdb:1285/1/2,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 1,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Normal Glucose Tolerance (NGT),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,44,13,1 month,16S,345,Roche454,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,"Table 2, Table S3 and Table S4",7 February 2025,NA,NA,The relative abundance of OTUs enriched in the NGT and T2DM groups.,decreased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales,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,k__Bacteria|k__Bacillati|p__Bacillota|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Megamonas,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Roseburia,k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota",2|3379134|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511;2|1783272|1239|186801|186802;2|3379134|1224|1236|135625|712|724;2|1783272|1239|186801|3085636|186803;2|1783272|1239|909932|909929|1843491|158846;2|1783272|1239|186801|3085636|186803|841;2|3379134|74201|203494;2|3379134|74201,Complete,NA +bsdb:1285/2/1,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Normal Glucose Tolerance (NGT),Prediabetes (Pre-DM),Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.,44,64,1 month,16S,345,Roche454,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S3 and Table S4,7 February 2025,NA,NA,The relative abundance of OTUs enriched in the NGT and PreDM groups.,increased,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,2|3379134|1224|28216,Complete,NA +bsdb:1285/2/2,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 2,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Normal Glucose Tolerance (NGT),Prediabetes (Pre-DM),Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.,44,64,1 month,16S,345,Roche454,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table S3 and Table S4,7 February 2025,NA,NA,The relative abundance of OTUs enriched in the NGT and PreDM groups.,decreased,"k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota",2|3379134|74201|203494;2|3379134|74201,Complete,NA +bsdb:1285/3/1,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Prediabetes (Pre-DM),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,64,13,1 month,16S,345,Roche454,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Table S3 and Table S4,7 February 2025,NA,NA,The relative abundance of OTUs enriched in the T2DM and PreDM groups.,increased,"k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota|c__Verrucomicrobiia,k__Bacteria|k__Pseudomonadati|p__Verrucomicrobiota",2|3379134|74201|203494;2|3379134|74201,Complete,NA +bsdb:1285/3/2,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 3,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Prediabetes (Pre-DM),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,64,13,1 month,16S,345,Roche454,Kruskall-Wallis,0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Table S3 and Table S4,7 February 2025,NA,NA,The relative abundance of OTUs enriched in the T2DM and PreDM groups.,decreased,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria,2|3379134|1224|28216,Complete,NA +bsdb:1285/4/1,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Normal Glucose Tolerance (NGT),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,44,13,1 month,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S4,7 February 2025,NA,NA,"Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",increased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|3379134|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|186806|1730;2|1783272|1239|186801|3082720|186804|1257;2|1783272|1239|186801|186802|216572|44748;2|1783272|1239|186801|186802|216572|292632;2|1783272|1239|186801|186802|216572|1263;2|1783272|1239|91061|186826|186827|46123,Complete,NA +bsdb:1285/4/2,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 4,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Normal Glucose Tolerance (NGT),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,44,13,1 month,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S4,7 February 2025,NA,NA,"Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",decreased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|3379134|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511,Complete,NA +bsdb:1285/5/1,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Normal Glucose Tolerance (NGT),Prediabetes (Pre-DM),Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.,44,64,1 month,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S4,7 February 2025,NA,NA,"Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",increased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|3379134|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|186802|216572|1263;2|1783272|1239|91061|186826|186827|46123,Complete,NA +bsdb:1285/5/2,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 5,China,Homo sapiens,Feces,UBERON:0001988,Prediabetes syndrome,EFO:1001121,Normal Glucose Tolerance (NGT),Prediabetes (Pre-DM),Prediabetes subjects including those with impaired fasting glucose and impaired glucose tolerance.,44,64,1 month,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S4,7 February 2025,NA,NA,"Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",decreased,"k__Bacteria|k__Pseudomonadati|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia",2|3379134|976|200643|171549|815|816;2|1783272|1239|186801|3085636|186803|572511,Complete,NA +bsdb:1285/6/1,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Prediabetes (Pre-DM),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,64,13,1 month,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 1,Figure S4,7 February 2025,NA,NA,"Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",increased,"k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Peptostreptococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Sporobacter,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Subdoligranulum,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Ruminococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia",2|1783272|1239|186801|186802|186806|1730;2|1783272|1239|186801|3085636|186803;2|1783272|1239|186801|3082720|186804|1257;2|1783272|1239|186801|186802|216572|44748;2|1783272|1239|186801|186802|216572|292632;2|1783272|1239|186801|186802|216572|1263;2|1783272|1239|91061|186826|186827|46123,Complete,NA +bsdb:1285/6/2,Study 1285,"cross-sectional observational, not case-control",24013136,10.1371/journal.pone.0071108,NA,"Zhang X, Shen D, Fang Z, Jie Z, Qiu X, Zhang C, Chen Y , Ji L",Human gut microbiota changes reveal the progression of glucose intolerance,PloS one,2013,NA,Experiment 6,China,Homo sapiens,Feces,UBERON:0001988,Diabetes mellitus,EFO:0000400,Prediabetes (Pre-DM),Type 2 diabetes mellitus (T2DM),Subjects with newly diagnosed Type 2 diabetes mellitus (T2DM).,64,13,1 month,16S,345,Roche454,Mann-Whitney (Wilcoxon),0.05,FALSE,NA,NA,NA,NA,unchanged,unchanged,NA,NA,NA,Signature 2,Figure S4,7 February 2025,NA,NA,"Changes in abundance for operational taxonomic units (OTUs,) that exhibited a significant difference in the Wilcoxon rank sum test between the NGT, Pre-DM, and T2DM groups.",decreased,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Lachnospirales|f__Lachnospiraceae|g__Blautia,2|1783272|1239|186801|3085636|186803|572511,Complete,NA bsdb:1286/1/NA,Study 1286,"cross-sectional observational, not case-control",39824829,10.1038/s41467-025-56014-6,NA,"Jeyaram K, Lahti L, Tims S, Heilig HGHJ, van Gelder AH, de Vos WM, Smidt H , Zoetendal EG",Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population,Nature communications,2025,NA,Experiment 1,India,Homo sapiens,Feces,UBERON:0001988,Phenotype,EFO:0000651,Group-A: never consumed Hawaijar and Dahi,NA,NA,20,NA,NA,16S,NA,Illumina,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA