Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets/Experiment 1

From BugSigDB


Needs review

Curated date: 2023/10/18

Curator: Winnie

Revision editor(s): Winnie

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled. Contact us to have more species added.
Mus musculus
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
Response to diet Response to diet,response to diet
Group 0 name Corresponds to the control (unexposed) group for case-control studies
mice on American diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
mice on ketogenic diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
male and female mice placed on American diet during feeding trial
Group 0 sample size Number of subjects in the control (unexposed) group
224
Group 1 sample size Number of subjects in the case (exposed) group
245

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
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).
relative abundances
Statistical test
ANOVA
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.001
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
sex, diet, Confounders controlled for: "genetic background" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.genetic background

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Needs review

Curated date: 2023/10/18

Curator: Winnie

Revision editor(s): Winnie, Davvve

Source: Fig. 4A

Description: Precision Nutrition through the integration of genetic variation, microbiota, and sex affecting microbiota variation

Abundance in Group 1: increased abundance in mice on ketogenic diet

NCBI Quality ControlLinks
Bilophila
Rikenella
Ruminiclostridium

Revision editor(s): Winnie, Davvve

Signature 2

Needs review

Curated date: 2023/10/18

Curator: Winnie

Revision editor(s): Winnie, Iram jamshed

Source: Fig. 4B

Description: Precision Nutrition through the integration of genetic variation, microbiota, and sex affecting microbiota variation

Abundance in Group 1: decreased abundance in mice on ketogenic diet

NCBI Quality ControlLinks
Parabacteroides
Rikenellaceae

Revision editor(s): Winnie, Iram jamshed