diff --git a/bugsigdb_signatures_genus_metaphlan.gmt b/bugsigdb_signatures_genus_metaphlan.gmt index 4f2acf141..b9888584b 100644 --- a/bugsigdb_signatures_genus_metaphlan.gmt +++ b/bugsigdb_signatures_genus_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -4419,18 +4419,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA k__Bacteria|p__Pseudomonadota|c__G bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia 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__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella 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__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus diff --git a/bugsigdb_signatures_genus_metaphlan_exact.gmt b/bugsigdb_signatures_genus_metaphlan_exact.gmt index f737e74c1..aec7843f2 100644 --- a/bugsigdb_signatures_genus_metaphlan_exact.gmt +++ b/bugsigdb_signatures_genus_metaphlan_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -3672,16 +3672,16 @@ bsdb:1060/17/2_Population:Tshwa_vs_Himba_DOWN NA k__Bacteria|p__Bacillota|c__Bac bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Campylobacterota|c__Epsilonproteobacteria|o__Campylobacterales|f__Campylobacteraceae|g__Campylobacter bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia diff --git a/bugsigdb_signatures_genus_ncbi.gmt b/bugsigdb_signatures_genus_ncbi.gmt index 0814b979f..a1d10d77b 100644 --- a/bugsigdb_signatures_genus_ncbi.gmt +++ b/bugsigdb_signatures_genus_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -4419,18 +4419,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA 590 194 544 bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA 46123 1386 1016 544 1870884 1716 1350 561 1378 724 2801844 bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA 848 1913599 bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA 71 1654 -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA 158483 544 1870884 1716 547 1350 561 570 286 508215 590 2529408 613 158876 +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA 158483 544 1870884 547 1350 561 286 508215 590 613 158876 bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA 71 1743 1654 32257 bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA 544 1350 570 561 32207 1870884 1716 1378 590 158876 1301 158483 848 47670 32257 547 543311 613 bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA 544 568 bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA 638847 -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 568 158483 547 158876 561 544 570 +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 158483 544 547 561 568 158876 bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA 568 547 158483 544 158876 561 590 32257 570 bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA 1654 bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA 568 1743 bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA 158483 544 547 158876 570 bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA 475 1016 -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158483 547 544 158876 570 848 32257 590 1913599 +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158483 544 547 158876 590 bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA 1016 475 32257 71 bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA 544 1743 bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA 46123 1386 1016 544 1870884 1716 1350 561 1378 724 diff --git a/bugsigdb_signatures_genus_ncbi_exact.gmt b/bugsigdb_signatures_genus_ncbi_exact.gmt index cf6996372..6a60f2845 100644 --- a/bugsigdb_signatures_genus_ncbi_exact.gmt +++ b/bugsigdb_signatures_genus_ncbi_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -3677,11 +3677,11 @@ bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA 71 1743 bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA 613 1378 47670 1350 544 547 561 590 158876 158483 1870884 bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA 568 bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA 638847 -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 568 158483 547 158876 561 544 +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 158483 544 547 561 568 158876 bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA 568 547 158483 544 158876 561 590 bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA 568 1743 bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA 158483 547 158876 544 -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158483 547 544 +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158483 544 547 158876 590 bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA 71 475 bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA 1743 bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA 46123 1386 1870884 1350 561 diff --git a/bugsigdb_signatures_genus_taxname.gmt b/bugsigdb_signatures_genus_taxname.gmt index 09ae1a0dd..0e4093249 100644 --- a/bugsigdb_signatures_genus_taxname.gmt +++ b/bugsigdb_signatures_genus_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -4419,18 +4419,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA Salmonella Campylobacter Citrobact bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA Abiotrophia Bacillus Capnocytophaga Citrobacter Clostridioides Corynebacterium Enterococcus Escherichia Gemella Haemophilus Arachnia bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA Fusobacterium Peptoanaerobacter bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA Simonsiella Actinomyces -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA Cedecea Citrobacter Clostridioides Corynebacterium Enterobacter Enterococcus Escherichia Klebsiella Pseudomonas Rothia Salmonella Schaalia Serratia Yokenella +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA Cedecea Citrobacter Clostridioides Enterobacter Enterococcus Escherichia Pseudomonas Rothia Salmonella Serratia Yokenella bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA Simonsiella Propionibacterium Actinomyces Kingella bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA Citrobacter Enterococcus Klebsiella Escherichia Rothia Clostridioides Corynebacterium Gemella Salmonella Yokenella Streptococcus Cedecea Fusobacterium Lautropia Kingella Enterobacter Parvimonas Serratia bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA Citrobacter Hafnia bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA Pyramidobacter -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Hafnia Cedecea Enterobacter Yokenella Escherichia Citrobacter Klebsiella +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Cedecea Citrobacter Enterobacter Escherichia Hafnia Yokenella bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA Hafnia Enterobacter Cedecea Citrobacter Yokenella Escherichia Salmonella Kingella Klebsiella bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA Actinomyces bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA Hafnia Propionibacterium bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA Cedecea Citrobacter Enterobacter Yokenella Klebsiella bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA Moraxella Capnocytophaga -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea Enterobacter Citrobacter Yokenella Klebsiella Fusobacterium Kingella Salmonella Peptoanaerobacter +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea Citrobacter Enterobacter Yokenella Salmonella bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA Capnocytophaga Moraxella Kingella Simonsiella bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA Citrobacter Propionibacterium bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA Abiotrophia Bacillus Capnocytophaga Citrobacter Clostridioides Corynebacterium Enterococcus Escherichia Gemella Haemophilus diff --git a/bugsigdb_signatures_genus_taxname_exact.gmt b/bugsigdb_signatures_genus_taxname_exact.gmt index e73b6b9c7..0a0f9d005 100644 --- a/bugsigdb_signatures_genus_taxname_exact.gmt +++ b/bugsigdb_signatures_genus_taxname_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -3677,11 +3677,11 @@ bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA Simonsiella Propionibacterium bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA Serratia Gemella Lautropia Enterococcus Citrobacter Enterobacter Escherichia Salmonella Yokenella Cedecea Clostridioides bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA Hafnia bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA Pyramidobacter -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Hafnia Cedecea Enterobacter Yokenella Escherichia Citrobacter +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Cedecea Citrobacter Enterobacter Escherichia Hafnia Yokenella bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA Hafnia Enterobacter Cedecea Citrobacter Yokenella Escherichia Salmonella bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA Hafnia Propionibacterium bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA Cedecea Enterobacter Yokenella Citrobacter -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea Enterobacter Citrobacter +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea Citrobacter Enterobacter Yokenella Salmonella bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA Simonsiella Moraxella bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA Propionibacterium bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA Abiotrophia Bacillus Clostridioides Enterococcus Escherichia diff --git a/bugsigdb_signatures_mixed_metaphlan.gmt b/bugsigdb_signatures_mixed_metaphlan.gmt index 401c6736a..3320a8eb6 100644 --- a/bugsigdb_signatures_mixed_metaphlan.gmt +++ b/bugsigdb_signatures_mixed_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -4893,18 +4893,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA k__Bacteria|p__Pseudomonadota|c__G bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes) bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria) k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria) k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp. k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp. k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes) diff --git a/bugsigdb_signatures_mixed_ncbi.gmt b/bugsigdb_signatures_mixed_ncbi.gmt index 8435f88e1..abc0e242c 100644 --- a/bugsigdb_signatures_mixed_ncbi.gmt +++ b/bugsigdb_signatures_mixed_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -4893,18 +4893,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA 590 194 1639133 1896336 bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA 46123 76631 1386 1017 546 1870884 1496 1720 1350 562 1379 84135 735 2801844 35517 1409 bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA 851 39498 bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA 72 55565 71 1654 -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA 158483 158484 544 546 545 1870884 1720 547 42895 1350 35783 561 571 573 576 286 508215 590 52768 613 616 158876 158877 +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA 158483 158484 544 546 545 1870884 1720 547 42895 1350 35783 561 571 573 576 286 508215 590 52768 613 616 158876 158877 562 bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA 71 1743 55565 504 72 bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA 546 35783 571 576 562 172042 573 545 1496 1720 84135 599 158877 1304 158484 1379 851 47671 505 42895 33033 613 1378 47670 1350 544 547 561 590 158876 158483 1870884 bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA 546 1873498 568 bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA 638847 638849 -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 568 158483 547 158876 158877 561 544 546 545 1639133 1896336 576 42895 571 158484 562 573 +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 158483 158484 544 546 545 1639133 1896336 547 42895 561 562 568 571 573 576 158876 158877 1873498 bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA 568 547 158483 544 158876 561 590 599 42895 505 562 573 158877 545 158484 1896336 546 571 576 1639133 1873498 bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA 55565 bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA 568 1873498 1743 bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA 158484 1639133 42895 158877 1896336 545 571 158483 547 158876 544 bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA 479 1017 -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158483 158484 547 544 546 545 1639133 1896336 158877 42895 571 851 505 599 39498 +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158483 158484 544 546 545 1639133 1896336 547 42895 851 505 571 599 158877 39498 158876 590 bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA 1017 479 504 72 71 475 bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA 1639133 1896336 1743 bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA 46123 76631 1386 1017 546 1870884 1496 1720 1350 561 562 1379 84135 735 35517 1409 diff --git a/bugsigdb_signatures_mixed_taxname.gmt b/bugsigdb_signatures_mixed_taxname.gmt index a67b665ba..8ecd4a978 100644 --- a/bugsigdb_signatures_mixed_taxname.gmt +++ b/bugsigdb_signatures_mixed_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -4893,18 +4893,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA Salmonella Campylobacter Citrobact bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA Abiotrophia Abiotrophia sp. Bacillus Capnocytophaga gingivalis Citrobacter freundii Clostridioides Clostridioides difficile Corynebacterium sp. Enterococcus Escherichia coli Gemella haemolysans Gemella sanguinis Haemophilus parahaemolyticus Arachnia [Eubacterium] brachy Bacillus sp. (in: firmicutes) bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA Fusobacterium nucleatum [Eubacterium] yurii bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA Simonsiella muelleri Actinomyces graevenitzii Simonsiella Actinomyces -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA Cedecea Cedecea davisae Citrobacter Citrobacter freundii Citrobacter koseri Clostridioides Corynebacterium sp. Enterobacter Enterobacter sp. Enterococcus Enterococcus sp. Escherichia Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Pseudomonas Rothia Salmonella Schaalia georgiae Serratia Serratia sp. (in: enterobacteria) Yokenella Yokenella regensburgei +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA Cedecea Cedecea davisae Citrobacter Citrobacter freundii Citrobacter koseri Clostridioides Corynebacterium sp. Enterobacter Enterobacter sp. Enterococcus Enterococcus sp. Escherichia Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Pseudomonas Rothia Salmonella Schaalia georgiae Serratia Serratia sp. (in: enterobacteria) Yokenella Yokenella regensburgei Escherichia coli bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA Simonsiella Propionibacterium Actinomyces graevenitzii Kingella kingae Simonsiella muelleri bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA Citrobacter freundii Enterococcus sp. Klebsiella oxytoca Klebsiella sp. Escherichia coli Rothia aeria Klebsiella pneumoniae Citrobacter koseri Clostridioides difficile Corynebacterium sp. Gemella sanguinis Salmonella sp. Yokenella regensburgei Streptococcus salivarius Cedecea davisae Gemella haemolysans Fusobacterium nucleatum Lautropia mirabilis Kingella oralis Enterobacter sp. Parvimonas micra Serratia Gemella Lautropia Enterococcus Citrobacter Enterobacter Escherichia Salmonella Yokenella Cedecea Clostridioides bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA Citrobacter freundii Hafnia sp. Hafnia bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA Pyramidobacter Pyramidobacter piscolens -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Hafnia Cedecea Enterobacter Yokenella Yokenella regensburgei Escherichia Citrobacter Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Klebsiella sp. Enterobacter sp. Klebsiella oxytoca Cedecea davisae Escherichia coli Klebsiella pneumoniae +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Cedecea Cedecea davisae Citrobacter Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Enterobacter Enterobacter sp. Escherichia Escherichia coli Hafnia Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Yokenella Yokenella regensburgei Hafnia sp. bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA Hafnia Enterobacter Cedecea Citrobacter Yokenella Escherichia Salmonella Salmonella sp. Enterobacter sp. Kingella oralis Escherichia coli Klebsiella pneumoniae Yokenella regensburgei Citrobacter koseri Cedecea davisae Citrobacter sp. Citrobacter freundii Klebsiella oxytoca Klebsiella sp. Citrobacter portucalensis Hafnia sp. bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA Actinomyces graevenitzii bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA Hafnia Hafnia sp. Propionibacterium bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA Cedecea davisae Citrobacter portucalensis Enterobacter sp. Yokenella regensburgei Citrobacter sp. Citrobacter koseri Klebsiella oxytoca Cedecea Enterobacter Yokenella Citrobacter bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA Moraxella sp. Capnocytophaga gingivalis -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea Cedecea davisae Enterobacter Citrobacter Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Yokenella regensburgei Enterobacter sp. Klebsiella oxytoca Fusobacterium nucleatum Kingella oralis Salmonella sp. [Eubacterium] yurii +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea Cedecea davisae Citrobacter Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Enterobacter Enterobacter sp. Fusobacterium nucleatum Kingella oralis Klebsiella oxytoca Salmonella sp. Yokenella regensburgei [Eubacterium] yurii Yokenella Salmonella bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA Capnocytophaga gingivalis Moraxella sp. Kingella kingae Simonsiella muelleri Simonsiella Moraxella bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA Citrobacter portucalensis Citrobacter sp. Propionibacterium bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA Abiotrophia Abiotrophia sp. Bacillus Capnocytophaga gingivalis Citrobacter freundii Clostridioides Clostridioides difficile Corynebacterium sp. Enterococcus Escherichia Escherichia coli Gemella haemolysans Gemella sanguinis Haemophilus parahaemolyticus [Eubacterium] brachy Bacillus sp. (in: firmicutes) diff --git a/bugsigdb_signatures_species_metaphlan.gmt b/bugsigdb_signatures_species_metaphlan.gmt index eafba7a59..0bddae190 100644 --- a/bugsigdb_signatures_species_metaphlan.gmt +++ b/bugsigdb_signatures_species_metaphlan.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae @@ -2121,18 +2121,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA k__Bacteria|p__Pseudomonadota|c__G bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes) bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria) k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria) k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp. k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp. k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes) diff --git a/bugsigdb_signatures_species_metaphlan_exact.gmt b/bugsigdb_signatures_species_metaphlan_exact.gmt index eafba7a59..0bddae190 100644 --- a/bugsigdb_signatures_species_metaphlan_exact.gmt +++ b/bugsigdb_signatures_species_metaphlan_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_14:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lacticaseibacillus|s__Lacticaseibacillus zeae @@ -2121,18 +2121,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA k__Bacteria|p__Pseudomonadota|c__G bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes) bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria) k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria) k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp. bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp. k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp. k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp. k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp. k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp. bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp. k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes) diff --git a/bugsigdb_signatures_species_ncbi.gmt b/bugsigdb_signatures_species_ncbi.gmt index 849754988..00ae79508 100644 --- a/bugsigdb_signatures_species_ncbi.gmt +++ b/bugsigdb_signatures_species_ncbi.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_11:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA 57037 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 57037 bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA 57037 @@ -2121,18 +2121,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA 1639133 1896336 bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA 76631 1017 546 1496 1720 562 1379 84135 735 35517 1409 bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA 851 39498 bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA 72 55565 -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA 158484 546 545 1720 42895 35783 571 573 576 52768 616 158877 +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA 158484 546 545 1720 42895 35783 571 573 576 52768 616 158877 562 bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA 55565 504 72 bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA 546 35783 571 576 562 172042 573 545 1496 1720 84135 599 158877 1304 158484 1379 851 47671 505 42895 33033 bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA 546 1873498 bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA 638849 -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 158877 546 545 1639133 1896336 576 42895 571 158484 562 573 +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 158484 546 545 1639133 1896336 42895 562 571 573 576 158877 1873498 bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA 599 42895 505 562 573 158877 545 158484 1896336 546 571 576 1639133 1873498 bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA 55565 bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA 1873498 bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA 158484 1639133 42895 158877 1896336 545 571 bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA 479 1017 -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158484 546 545 1639133 1896336 158877 42895 571 851 505 599 39498 +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158484 546 545 1639133 1896336 42895 851 505 571 599 158877 39498 bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA 1017 479 504 72 bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA 1639133 1896336 bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA 76631 1017 546 1496 1720 562 1379 84135 735 35517 1409 diff --git a/bugsigdb_signatures_species_ncbi_exact.gmt b/bugsigdb_signatures_species_ncbi_exact.gmt index 849754988..00ae79508 100644 --- a/bugsigdb_signatures_species_ncbi_exact.gmt +++ b/bugsigdb_signatures_species_ncbi_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_11:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA 57037 bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA 57037 bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA 57037 @@ -2121,18 +2121,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA 1639133 1896336 bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA 76631 1017 546 1496 1720 562 1379 84135 735 35517 1409 bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA 851 39498 bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA 72 55565 -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA 158484 546 545 1720 42895 35783 571 573 576 52768 616 158877 +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA 158484 546 545 1720 42895 35783 571 573 576 52768 616 158877 562 bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA 55565 504 72 bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA 546 35783 571 576 562 172042 573 545 1496 1720 84135 599 158877 1304 158484 1379 851 47671 505 42895 33033 bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA 546 1873498 bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA 638849 -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 158877 546 545 1639133 1896336 576 42895 571 158484 562 573 +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA 158484 546 545 1639133 1896336 42895 562 571 573 576 158877 1873498 bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA 599 42895 505 562 573 158877 545 158484 1896336 546 571 576 1639133 1873498 bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA 55565 bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA 1873498 bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA 158484 1639133 42895 158877 1896336 545 571 bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA 479 1017 -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158484 546 545 1639133 1896336 158877 42895 571 851 505 599 39498 +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA 158484 546 545 1639133 1896336 42895 851 505 571 599 158877 39498 bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA 1017 479 504 72 bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA 1639133 1896336 bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA 76631 1017 546 1496 1720 562 1379 84135 735 35517 1409 diff --git a/bugsigdb_signatures_species_taxname.gmt b/bugsigdb_signatures_species_taxname.gmt index 2ac81cf2d..9bb5f52b4 100644 --- a/bugsigdb_signatures_species_taxname.gmt +++ b/bugsigdb_signatures_species_taxname.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_13:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA Lacticaseibacillus zeae bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Lacticaseibacillus zeae bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA Lacticaseibacillus zeae @@ -2121,18 +2121,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA Citrobacter portucalensis Citrobac bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA Abiotrophia sp. Capnocytophaga gingivalis Citrobacter freundii Clostridioides difficile Corynebacterium sp. Escherichia coli Gemella haemolysans Gemella sanguinis Haemophilus parahaemolyticus [Eubacterium] brachy Bacillus sp. (in: firmicutes) bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA Fusobacterium nucleatum [Eubacterium] yurii bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA Simonsiella muelleri Actinomyces graevenitzii -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA Cedecea davisae Citrobacter freundii Citrobacter koseri Corynebacterium sp. Enterobacter sp. Enterococcus sp. Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Schaalia georgiae Serratia sp. (in: enterobacteria) Yokenella regensburgei +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA Cedecea davisae Citrobacter freundii Citrobacter koseri Corynebacterium sp. Enterobacter sp. Enterococcus sp. Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Schaalia georgiae Serratia sp. (in: enterobacteria) Yokenella regensburgei Escherichia coli bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA Actinomyces graevenitzii Kingella kingae Simonsiella muelleri bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA Citrobacter freundii Enterococcus sp. Klebsiella oxytoca Klebsiella sp. Escherichia coli Rothia aeria Klebsiella pneumoniae Citrobacter koseri Clostridioides difficile Corynebacterium sp. Gemella sanguinis Salmonella sp. Yokenella regensburgei Streptococcus salivarius Cedecea davisae Gemella haemolysans Fusobacterium nucleatum Lautropia mirabilis Kingella oralis Enterobacter sp. Parvimonas micra bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA Citrobacter freundii Hafnia sp. bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA Pyramidobacter piscolens -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Yokenella regensburgei Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Klebsiella sp. Enterobacter sp. Klebsiella oxytoca Cedecea davisae Escherichia coli Klebsiella pneumoniae +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Cedecea davisae Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Enterobacter sp. Escherichia coli Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Yokenella regensburgei Hafnia sp. bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA Salmonella sp. Enterobacter sp. Kingella oralis Escherichia coli Klebsiella pneumoniae Yokenella regensburgei Citrobacter koseri Cedecea davisae Citrobacter sp. Citrobacter freundii Klebsiella oxytoca Klebsiella sp. Citrobacter portucalensis Hafnia sp. bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA Actinomyces graevenitzii bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA Hafnia sp. bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA Cedecea davisae Citrobacter portucalensis Enterobacter sp. Yokenella regensburgei Citrobacter sp. Citrobacter koseri Klebsiella oxytoca bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA Moraxella sp. Capnocytophaga gingivalis -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea davisae Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Yokenella regensburgei Enterobacter sp. Klebsiella oxytoca Fusobacterium nucleatum Kingella oralis Salmonella sp. [Eubacterium] yurii +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea davisae Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Enterobacter sp. Fusobacterium nucleatum Kingella oralis Klebsiella oxytoca Salmonella sp. Yokenella regensburgei [Eubacterium] yurii bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA Capnocytophaga gingivalis Moraxella sp. Kingella kingae Simonsiella muelleri bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA Citrobacter portucalensis Citrobacter sp. bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA Abiotrophia sp. Capnocytophaga gingivalis Citrobacter freundii Clostridioides difficile Corynebacterium sp. Escherichia coli Gemella haemolysans Gemella sanguinis Haemophilus parahaemolyticus [Eubacterium] brachy Bacillus sp. (in: firmicutes) diff --git a/bugsigdb_signatures_species_taxname_exact.gmt b/bugsigdb_signatures_species_taxname_exact.gmt index 2ac81cf2d..9bb5f52b4 100644 --- a/bugsigdb_signatures_species_taxname_exact.gmt +++ b/bugsigdb_signatures_species_taxname_exact.gmt @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_13:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org bsdb:1/1/1_Colorectal-adenoma:conventional-adenoma-cases_vs_controls_UP NA Lacticaseibacillus zeae bsdb:1/2/1_Hyperplastic-Polyp:hyperplastic-polyp-cases_vs_controls_UP NA Lacticaseibacillus zeae bsdb:1/6/1_Colorectal-adenoma:Non-advanced-conventional-adenoma-cases_vs_controls_UP NA Lacticaseibacillus zeae @@ -2121,18 +2121,18 @@ bsdb:1060/18/1_Population:!Xun_vs_Himba_UP NA Citrobacter portucalensis Citrobac bsdb:1060/18/2_Population:!Xun_vs_Himba_DOWN NA Abiotrophia sp. Capnocytophaga gingivalis Citrobacter freundii Clostridioides difficile Corynebacterium sp. Escherichia coli Gemella haemolysans Gemella sanguinis Haemophilus parahaemolyticus [Eubacterium] brachy Bacillus sp. (in: firmicutes) bsdb:1060/19/1_Population:Tshwa_vs_Twa_UP NA Fusobacterium nucleatum [Eubacterium] yurii bsdb:1060/19/2_Population:Tshwa_vs_Twa_DOWN NA Simonsiella muelleri Actinomyces graevenitzii -bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA Cedecea davisae Citrobacter freundii Citrobacter koseri Corynebacterium sp. Enterobacter sp. Enterococcus sp. Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Schaalia georgiae Serratia sp. (in: enterobacteria) Yokenella regensburgei +bsdb:1060/20/1_Population:!Xun_vs_Twa_DOWN NA Cedecea davisae Citrobacter freundii Citrobacter koseri Corynebacterium sp. Enterobacter sp. Enterococcus sp. Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Schaalia georgiae Serratia sp. (in: enterobacteria) Yokenella regensburgei Escherichia coli bsdb:1060/21/1_Population:!Xun_vs_Tshwa_UP NA Actinomyces graevenitzii Kingella kingae Simonsiella muelleri bsdb:1060/21/2_Population:!Xun_vs_Tshwa_DOWN NA Citrobacter freundii Enterococcus sp. Klebsiella oxytoca Klebsiella sp. Escherichia coli Rothia aeria Klebsiella pneumoniae Citrobacter koseri Clostridioides difficile Corynebacterium sp. Gemella sanguinis Salmonella sp. Yokenella regensburgei Streptococcus salivarius Cedecea davisae Gemella haemolysans Fusobacterium nucleatum Lautropia mirabilis Kingella oralis Enterobacter sp. Parvimonas micra bsdb:1060/22/1_Population:Kwisi_vs_Tjimba_UP NA Citrobacter freundii Hafnia sp. bsdb:1060/22/2_Population:Kwisi_vs_Tjimba_UP NA Pyramidobacter piscolens -bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Yokenella regensburgei Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Klebsiella sp. Enterobacter sp. Klebsiella oxytoca Cedecea davisae Escherichia coli Klebsiella pneumoniae +bsdb:1060/23/1_Population:Twa_vs_Tjimba_UP NA Cedecea davisae Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Enterobacter sp. Escherichia coli Klebsiella oxytoca Klebsiella pneumoniae Klebsiella sp. Yokenella regensburgei Hafnia sp. bsdb:1060/24/1_Population:Tshwa_vs_Tjimba_UP NA Salmonella sp. Enterobacter sp. Kingella oralis Escherichia coli Klebsiella pneumoniae Yokenella regensburgei Citrobacter koseri Cedecea davisae Citrobacter sp. Citrobacter freundii Klebsiella oxytoca Klebsiella sp. Citrobacter portucalensis Hafnia sp. bsdb:1060/24/2_Population:Tshwa_vs_Tjimba_UP NA Actinomyces graevenitzii bsdb:1060/25/1_Population:!Xun_vs_Tjimba_UP NA Hafnia sp. bsdb:1060/26/1_Population:Twa_vs_Kwisi_UP NA Cedecea davisae Citrobacter portucalensis Enterobacter sp. Yokenella regensburgei Citrobacter sp. Citrobacter koseri Klebsiella oxytoca bsdb:1060/26/2_Population:Twa_vs_Kwisi_DOWN NA Moraxella sp. Capnocytophaga gingivalis -bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea davisae Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Yokenella regensburgei Enterobacter sp. Klebsiella oxytoca Fusobacterium nucleatum Kingella oralis Salmonella sp. [Eubacterium] yurii +bsdb:1060/27/1_Population:Tshwa_vs_Kwisi_UP NA Cedecea davisae Citrobacter freundii Citrobacter koseri Citrobacter portucalensis Citrobacter sp. Enterobacter sp. Fusobacterium nucleatum Kingella oralis Klebsiella oxytoca Salmonella sp. Yokenella regensburgei [Eubacterium] yurii bsdb:1060/27/2_Population:Tshwa_vs_Kwisi_DOWN NA Capnocytophaga gingivalis Moraxella sp. Kingella kingae Simonsiella muelleri bsdb:1060/28/1_Population:!Xun_vs_Kwisi_UP NA Citrobacter portucalensis Citrobacter sp. bsdb:1060/28/2_Population:!Xun_vs_Kwisi_DOWN NA Abiotrophia sp. Capnocytophaga gingivalis Citrobacter freundii Clostridioides difficile Corynebacterium sp. Escherichia coli Gemella haemolysans Gemella sanguinis Haemophilus parahaemolyticus [Eubacterium] brachy Bacillus sp. (in: firmicutes) diff --git a/file_size.csv b/file_size.csv index 1c8ef323d..b0ba1f31f 100644 --- a/file_size.csv +++ b/file_size.csv @@ -2443,3 +2443,4 @@ "2025-01-10_14:58_UTC" "4901" "5754" "4901" "5754" "4901" "5754" "6665" "6665" "6665" "3018" "3018" "3018" "3018" "3018" "3018" "4499" "7773" "7378" "1368" "2025-01-10_15:58_UTC" "4900" "5753" "4900" "5753" "4900" "5753" "6664" "6664" "6664" "3018" "3018" "3018" "3018" "3018" "3018" "4498" "7772" "7377" "1368" "2025-01-10_16:58_UTC" "4900" "5753" "4900" "5753" "4900" "5753" "6664" "6664" "6664" "3018" "3018" "3018" "3018" "3018" "3018" "4498" "7772" "7377" "1368" +"2025-01-10_17:58_UTC" "4900" "5753" "4900" "5753" "4900" "5753" "6664" "6664" "6664" "3018" "3018" "3018" "3018" "3018" "3018" "4498" "7772" "7377" "1368" diff --git a/full_dump.csv b/full_dump.csv index 6298a0cce..43a1cdf74 100644 --- a/full_dump.csv +++ b/full_dump.csv @@ -1,4 +1,4 @@ -# BugSigDB 2025-01-10_15:58_UTC, License: Creative Commons Attribution 4.0 International, URL: https://bugsigdb.org +# BugSigDB 2025-01-10_17:58_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 @@ -5770,18 +5770,18 @@ bsdb:1060/18/1,Study 1060,"cross-sectional observational, not case-control",3759 bsdb:1060/18/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 18,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Himba,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Arachnia,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes)",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|76631;2|1239|91061|1385|186817|1386;2|976|117743|200644|49546|1016|1017;2|1224|1236|91347|543|544|546;2|1239|186801|3082720|186804|1870884;2|1239|186801|3082720|186804|1870884|1496;2|201174|1760|85007|1653|1716|1720;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561|562;2|1239|91061|1385|539738|1378|1379;2|1239|91061|1385|539738|1378|84135;2|1224|1236|135625|712|724|735;2|201174|1760|85009|31957|2801844;2|1239|186801|186802|543314|35517;2|1239|91061|1385|186817|1386|1409,Complete,NA bsdb:1060/19/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 19,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,Tshwa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",2|32066|203490|203491|203492|848|851;2|1239|186801|3082720|3118655|1913599|39498,Complete,NA bsdb:1060/19/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 19,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,Tshwa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",7,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,"Supplementary Table 4 and 5, Figure 5",25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces",2|1224|28216|206351|481|71|72;2|201174|1760|2037|2049|1654|55565;2|1224|28216|206351|481|71;2|201174|1760|2037|2049|1654,Complete,NA -bsdb:1060/20/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 20,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria),k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei",2|1224|1236|91347|543|158483;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|545;2|1239|186801|3082720|186804|1870884;2|201174|1760|85007|1653|1716|1720;2|1224|1236|91347|543|547;2|1224|1236|91347|543|547|42895;2|1239|91061|186826|81852|1350;2|1239|91061|186826|81852|1350|35783;2|1224|1236|91347|543|561;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|570|576;2|1224|1236|72274|135621|286;2759|33090|35493|3398|72025|3803|3814|508215;2|1224|1236|91347|543|590;2|201174|1760|2037|2049|2529408|52768;2|1224|1236|91347|1903411|613;2|1224|1236|91347|1903411|613|616;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877,Complete,NA +bsdb:1060/20/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 20,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Twa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",7,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|k__Bacillati|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas,k__Eukaryota|k__Viridiplantae|p__Streptophyta|c__Magnoliopsida|o__Fabales|f__Fabaceae|s__Papilionoideae|g__Rothia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|k__Bacillati|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Schaalia|s__Schaalia georgiae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia|s__Serratia sp. (in: enterobacteria),k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli",2|3379134|1224|1236|91347|543|158483;2|3379134|1224|1236|91347|543|158483|158484;2|3379134|1224|1236|91347|543|544;2|3379134|1224|1236|91347|543|544|546;2|3379134|1224|1236|91347|543|544|545;2|1783272|1239|186801|3082720|186804|1870884;2|1783272|201174|1760|85007|1653|1716|1720;2|3379134|1224|1236|91347|543|547;2|3379134|1224|1236|91347|543|547|42895;2|1783272|1239|91061|186826|81852|1350;2|1783272|1239|91061|186826|81852|1350|35783;2|3379134|1224|1236|91347|543|561;2|3379134|1224|1236|91347|543|570|571;2|3379134|1224|1236|91347|543|570|573;2|3379134|1224|1236|91347|543|570|576;2|3379134|1224|1236|72274|135621|286;2759|33090|35493|3398|72025|3803|3814|508215;2|3379134|1224|1236|91347|543|590;2|1783272|201174|1760|2037|2049|2529408|52768;2|3379134|1224|1236|91347|1903411|613;2|3379134|1224|1236|91347|1903411|613|616;2|3379134|1224|1236|91347|543|158876;2|3379134|1224|1236|91347|543|158876|158877;2|3379134|1224|1236|91347|543|561|562,Complete,NA bsdb:1060/21/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 21,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tshwa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",5,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 1,"Supplementary Table 4 and 5, Figure 5",25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri",2|1224|28216|206351|481|71;2|201174|1760|85009|31957|1743;2|201174|1760|2037|2049|1654|55565;2|1224|28216|206351|481|32257|504;2|1224|28216|206351|481|71|72,Complete,NA bsdb:1060/21/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 21,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tshwa,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups.",5,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,increased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia aeria,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus salivarius,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia|s__Lautropia mirabilis,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Bacillota|c__Tissierellia|o__Tissierellales|f__Peptoniphilaceae|g__Parvimonas|s__Parvimonas micra,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Yersiniaceae|g__Serratia,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiaceae|g__Lautropia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides",2|1224|1236|91347|543|544|546;2|1239|91061|186826|81852|1350|35783;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|576;2|1224|1236|91347|543|561|562;2|201174|1760|85006|1268|32207|172042;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|544|545;2|1239|186801|3082720|186804|1870884|1496;2|201174|1760|85007|1653|1716|1720;2|1239|91061|1385|539738|1378|84135;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|158876|158877;2|1239|91061|186826|1300|1301|1304;2|1224|1236|91347|543|158483|158484;2|1239|91061|1385|539738|1378|1379;2|32066|203490|203491|203492|848|851;2|1224|28216|80840|119060|47670|47671;2|1224|28216|206351|481|32257|505;2|1224|1236|91347|543|547|42895;2|1239|1737404|1737405|1570339|543311|33033;2|1224|1236|91347|1903411|613;2|1239|91061|1385|539738|1378;2|1224|28216|80840|119060|47670;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|544;2|1224|1236|91347|543|547;2|1224|1236|91347|543|561;2|1224|1236|91347|543|590;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158483;2|1239|186801|3082720|186804|1870884,Complete,NA bsdb:1060/22/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 22,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,4,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia",2|1224|1236|91347|543|544|546;2|1224|1236|91347|1903412|568|1873498;2|1224|1236|91347|1903412|568,Complete,NA bsdb:1060/22/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 22,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Kwisi,The Kwisi are a marginalized group whose origins have been considered enigmatic. Their livelihoods also deviate from traditional food production or foraging patterns.,4,8,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter,k__Bacteria|p__Synergistota|c__Synergistia|o__Synergistales|f__Dethiosulfovibrionaceae|g__Pyramidobacter|s__Pyramidobacter piscolens",2|508458|649775|649776|3029088|638847;2|508458|649775|649776|3029088|638847|638849,Complete,NA -bsdb:1060/23/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 23,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",4,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae",2|1224|1236|91347|1903412|568;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|561;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|570|576;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|573,Complete,NA +bsdb:1060/23/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 23,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",4,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.",2|3379134|1224|1236|91347|543|158483;2|3379134|1224|1236|91347|543|158483|158484;2|3379134|1224|1236|91347|543|544;2|3379134|1224|1236|91347|543|544|546;2|3379134|1224|1236|91347|543|544|545;2|3379134|1224|1236|91347|543|544|1639133;2|3379134|1224|1236|91347|543|544|1896336;2|3379134|1224|1236|91347|543|547;2|3379134|1224|1236|91347|543|547|42895;2|3379134|1224|1236|91347|543|561;2|3379134|1224|1236|91347|543|561|562;2|3379134|1224|1236|91347|1903412|568;2|3379134|1224|1236|91347|543|570|571;2|3379134|1224|1236|91347|543|570|573;2|3379134|1224|1236|91347|543|570|576;2|3379134|1224|1236|91347|543|158876;2|3379134|1224|1236|91347|543|158876|158877;2|3379134|1224|1236|91347|1903412|568|1873498,Complete,NA bsdb:1060/24/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 24,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",4,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella pneumoniae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.",2|1224|1236|91347|1903412|568;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|544;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|561;2|1224|1236|91347|543|590;2|1224|1236|91347|543|590|599;2|1224|1236|91347|543|547|42895;2|1224|28216|206351|481|32257|505;2|1224|1236|91347|543|561|562;2|1224|1236|91347|543|570|573;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|570|576;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|1903412|568|1873498,Complete,NA bsdb:1060/24/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 24,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",4,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second population.",increased,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces graevenitzii,2|201174|1760|2037|2049|1654|55565,Complete,NA bsdb:1060/25/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 25,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Tjimba,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",4,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Hafniaceae|g__Hafnia|s__Hafnia sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|1224|1236|91347|1903412|568;2|1224|1236|91347|1903412|568|1873498;2|201174|1760|85009|31957|1743,Complete,NA bsdb:1060/26/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 26,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",8,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter",2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|570|571;2|1224|1236|91347|543|158483;2|1224|1236|91347|543|547;2|1224|1236|91347|543|158876;2|1224|1236|91347|543|544,Complete,NA bsdb:1060/26/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 26,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Twa,"The Twa are a marginalized group in the region, describing themselves as the indigenous people of the area. Their livelihoods do not conform to traditional food production or foraging patterns.",8,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis",2|1224|1236|2887326|468|475|479;2|976|117743|200644|49546|1016|1017,Complete,NA -bsdb:1060/27/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 27,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",8,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii",2|1224|1236|91347|543|158483;2|1224|1236|91347|543|158483|158484;2|1224|1236|91347|543|547;2|1224|1236|91347|543|544;2|1224|1236|91347|543|544|546;2|1224|1236|91347|543|544|545;2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336;2|1224|1236|91347|543|158876|158877;2|1224|1236|91347|543|547|42895;2|1224|1236|91347|543|570|571;2|32066|203490|203491|203492|848|851;2|1224|28216|206351|481|32257|505;2|1224|1236|91347|543|590|599;2|1239|186801|3082720|3118655|1913599|39498,Complete,NA +bsdb:1060/27/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 27,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",8,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Cedecea|s__Cedecea davisae,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter koseri,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter|s__Enterobacter sp.,k__Bacteria|k__Fusobacteriati|p__Fusobacteriota|c__Fusobacteriia|o__Fusobacteriales|f__Fusobacteriaceae|g__Fusobacterium|s__Fusobacterium nucleatum,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella oralis,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Klebsiella|s__Klebsiella oxytoca,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella|s__Salmonella sp.,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella|s__Yokenella regensburgei,k__Bacteria|k__Bacillati|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Filifactoraceae|g__Peptoanaerobacter|s__[Eubacterium] yurii,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Yokenella,k__Bacteria|k__Pseudomonadati|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Salmonella",2|3379134|1224|1236|91347|543|158483;2|3379134|1224|1236|91347|543|158483|158484;2|3379134|1224|1236|91347|543|544;2|3379134|1224|1236|91347|543|544|546;2|3379134|1224|1236|91347|543|544|545;2|3379134|1224|1236|91347|543|544|1639133;2|3379134|1224|1236|91347|543|544|1896336;2|3379134|1224|1236|91347|543|547;2|3379134|1224|1236|91347|543|547|42895;2|3384189|32066|203490|203491|203492|848|851;2|3379134|1224|28216|206351|481|32257|505;2|3379134|1224|1236|91347|543|570|571;2|3379134|1224|1236|91347|543|590|599;2|3379134|1224|1236|91347|543|158876|158877;2|1783272|1239|186801|3082720|3118655|1913599|39498;2|3379134|1224|1236|91347|543|158876;2|3379134|1224|1236|91347|543|590,Complete,NA bsdb:1060/27/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 27,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,Tshwa,"Khoe-Kwadi-speaking foragers from the Tsholotsho District of western Zimbabwe. They traditionally relied on foraging but were forced to leave their hunting grounds in Hwange National Park during the early 20th century, leading to social marginalization.",8,5,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,decreased,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella|s__Moraxella sp.,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Kingella|s__Kingella kingae,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella|s__Simonsiella muelleri,k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Simonsiella,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Moraxellales|f__Moraxellaceae|g__Moraxella",2|976|117743|200644|49546|1016|1017;2|1224|1236|2887326|468|475|479;2|1224|28216|206351|481|32257|504;2|1224|28216|206351|481|71|72;2|1224|28216|206351|481|71;2|1224|1236|2887326|468|475,Complete,NA bsdb:1060/28/1,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 28,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",8,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 1,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",increased,"k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter portucalensis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter sp.,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium",2|1224|1236|91347|543|544|1639133;2|1224|1236|91347|543|544|1896336;2|201174|1760|85009|31957|1743,Complete,NA bsdb:1060/28/2,Study 1060,"cross-sectional observational, not case-control",37596536,10.1186/s12866-023-02970-2,NA,"Araújo V, Fehn AM, Phiri A, Wills J, Rocha J , Gayà-Vidal M",Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe,BMC microbiology,2023,"African populations, Exome sequencing, Metagenomics, Oral microbiome, Oral microbiota, Saliva, Socio-economic status, Subsistence methods",Experiment 28,"Angola,Zimbabwe",Homo sapiens,Saliva,UBERON:0001836,Population,IDOMAL:0001254,Kwisi,!Xun,"The !Xun are Kx’a-speaking foragers residing in neighboring Kunene Province in Angola. They inhabit areas characterized by open savanna woodland, differing from the coastal plains occupied by the other groups",8,7,NA,16S,12,Illumina,DESeq2,0.05,TRUE,NA,NA,NA,NA,unchanged,NA,NA,NA,NA,Signature 2,Supplementary Table 4 and 5,25 March 2024,MyleeeA,MyleeeA,"Differential abundance (FDR adjusted p_value <0.05) between populations according to DESeq2 analysis. Positive values in the log2FoldChange indicate taxa enriched in the first population of the comparison, and negative values represent taxa enriched in the second one.",decreased,"k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus,k__Bacteria|p__Bacteroidota|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Capnocytophaga|s__Capnocytophaga gingivalis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter|s__Citrobacter freundii,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides,k__Bacteria|p__Bacillota|c__Clostridia|o__Peptostreptococcales|f__Peptostreptococcaceae|g__Clostridioides|s__Clostridioides difficile,k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp.,k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia coli,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella haemolysans,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Gemellaceae|g__Gemella|s__Gemella sanguinis,k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus|s__Haemophilus parahaemolyticus,k__Bacteria|p__Bacillota|c__Clostridia|o__Eubacteriales|f__Eubacteriales Family XIII. Incertae Sedis|s__[Eubacterium] brachy,k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus sp. (in: firmicutes)",2|1239|91061|186826|186827|46123;2|1239|91061|186826|186827|46123|76631;2|1239|91061|1385|186817|1386;2|976|117743|200644|49546|1016|1017;2|1224|1236|91347|543|544|546;2|1239|186801|3082720|186804|1870884;2|1239|186801|3082720|186804|1870884|1496;2|201174|1760|85007|1653|1716|1720;2|1239|91061|186826|81852|1350;2|1224|1236|91347|543|561;2|1224|1236|91347|543|561|562;2|1239|91061|1385|539738|1378|1379;2|1239|91061|1385|539738|1378|84135;2|1224|1236|135625|712|724|735;2|1239|186801|186802|543314|35517;2|1239|91061|1385|186817|1386|1409,Complete,NA