Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas/Experiment 3
From BugSigDB
Needs review
Subjects
- Location of subjects
- Ethiopia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Theropithecus gelada
- 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
- Reproductive behaviour measurement Reproductive behaviour measurement,reproductive behaviour measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cycling females
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pregnant females
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant females refers to female at their pregnancy reproductive state. It started on the date of conception and ended the day before parturition.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 158
- Group 1 sample size Number of subjects in the case (exposed) group
- 61
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).
- centered log-ratio
- Statistical test
- Mixed-Effects Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
- Confounders controlled for: "individual membership" 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.individual membership, Confounders controlled for: "unit membership" 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.unit membership
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Needs review
Source: Table S13
Description: Differential abundance of taxa between pregnant and cycling female geladas
Abundance in Group 1: increased abundance in Pregnant females
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacterales | ||
| Campylobacterota | ||
| Epsilonproteobacteria | ||
| Helicobacter | ||
| Helicobacteraceae | ||
| Thomasclavelia | ||
| Verrucomicrobiia | ||
| Verrucomicrobiota | ||
| [Ruminococcus] torques |
Revision editor(s): KateRasheed
