Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes/Experiment 2
From BugSigDB
Subjects
- Location of subjects
- United States of America
- 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
- Diabetes mellitus biomarker Diabetes mellitus biomarker,diabetes mellitus biomarker
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls in ET-B
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 diabetes (T2DM) in ET-B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants were Caucasians with T2DM aged over 30 years. (ET-B).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 416
- Group 1 sample size Number of subjects in the case (exposed) group
- 533
Lab analysis
- Sequencing type
- 16S
- 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).
- relative abundances
- Statistical test
- Decision Trees (xgBoost Statistical test: "Decision Trees (xgBoost" is not in the list (ANCOM, ANCOM-BC, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Decision Trees (xgBoost, gradient boosting), Dunn's test, DESeq2, ...) of allowed values.
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3B
Description: Fecal bacteria composition in Enterotype Bacteroidaceae (ET-B)
Abundance in Group 1: increased abundance in Type 2 diabetes (T2DM) in ET-B
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter ruminantium | ||
| Bacteroides koreensis | ||
| Agathobacter rectalis |
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 3B
Description: Fecal bacteria composition in Enterotype Bacteroidaceae (ET-B)
Abundance in Group 1: decreased abundance in Type 2 diabetes (T2DM) in ET-B
Revision editor(s): Miss Lulu
