Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by KateRasheed on 2025-6-23

Curated date: 2025/03/16

Curator: KateRasheed

Revision editor(s): KateRasheed

Subjects

Location of subjects
Germany
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Diet measurement Diet measurement,diet measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Vegan
Group 1 name Corresponds to the case (exposed) group for case-control studies
Omnivore
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Omnivore refers to individuals regularly consuming a mixed diet of meat and meat products of ≥170 g/day).
Group 0 sample size Number of subjects in the control (unexposed) group
33
Group 1 sample size Number of subjects in the case (exposed) group
28

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
arcsine square-root
Statistical test
MaAsLin2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.25
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
Matched on Factors on which subjects have been matched on in a case-control study
age, sex


Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-6-23

Curated date: 2025/03/17

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Supplementary Table 3A

Description: A panel of species that were differentially abundant in one diet type compared to the other.

Abundance in Group 1: decreased abundance in Omnivore

NCBI Quality ControlLinks
Blautia sp. MSK.21.1
Clostridia bacterium
Clostridium sp. AF20-17LB
Coprococcus eutactus
Eubacterium ramulus
Lachnospiraceae bacterium
Lachnospiraceae bacterium OF09-6
Lachnospiraceae bacterium OM04-12BH
Ruminococcus callidus
Ruminococcus sp. AF41-9
GGB9615_SGB15052GGB9615_SGB15052
Lachnospira_SGB5076Lachnospira_SGB5076
GGB3486_SGB4658GGB3486_SGB4658
GGB4456_SGB6141GGB4456_SGB6141
GGB51441_SGB71759GGB51441_SGB71759
GGB9618_SGB15065GGB9618_SGB15065
Lachnospira sp. NSJ-43Lachnospira sp. NSJ-43

Revision editor(s): KateRasheed

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-23

Curated date: 2025/03/17

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Supplementary Table 3A

Description: A panel of species that were differentially abundant in one diet type compared to the other.

Abundance in Group 1: increased abundance in Omnivore

NCBI Quality ControlLinks
Alistipes inops
Allisonella histaminiformans
Anaeromassilibacillus sp. An250
Bilophila wadsworthia
Blautia faecis
Blautia wexlerae
Candidatus Borkfalkia ceftriaxoniphila
Candidatus Pseudobutyricicoccus lothianensis
Clostridia bacterium
Clostridiaceae bacterium
Clostridiales bacterium
Clostridium phoceensis
Dysosmobacter welbionis
Evtepia gabavorous
Flavonifractor plautii
Lactococcus lactis
Mediterraneibacter glycyrrhizinilyticus
Merdimmobilis hominis
Odoribacter splanchnicus
Oscillospiraceae bacterium
Thomasclavelia ramosa
[Ruminococcus] lactaris
GGB9186_SGB14125GGB9186_SGB14125
Ruminococcaceae_unclassified_SGB4191Ruminococcaceae_unclassified_SGB4191
GGB3005_SGB3996GGB3005_SGB3996
GGB9818_SGB15459GGB9818_SGB15459
GGB3034_SGB4030GGB3034_SGB4030
Clostridia_unclassified_SGB14844Clostridia_unclassified_SGB14844
GGB45620_SGB63333GGB45620_SGB63333
GGB6601_SGB9333GGB6601_SGB9333
GGB45432_SGB63101GGB45432_SGB63101
Eggerthellaceae_unclassified_SGB14341Eggerthellaceae_unclassified_SGB14341
GGB9667_SGB15164GGB9667_SGB15164
Dysosmobacter sp. NSJ-60Dysosmobacter sp. NSJ-60

Revision editor(s): KateRasheed