Changes in social environment impact primate gut microbiota composition/Experiment 1
Subjects
- Location of subjects
- Canada
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Macaca fascicularis
- 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 Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Uncontrolled diet (T1 single)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Controlled diet (T2 single)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Following T1Single data collection, at the beginning of the Single Living phase, the enrichment elements of NHP’s diet for the remainder of the study (referred to as “controlled” diet) was strictly controlled. This controlled diet approach directly help to investigate how diet alterations impact GM composition during a period of stable single living, i.e., comparing the transition from uncontrolled (T1Single) to controlled diet (T2Single) during the Single Living phase.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 2C and Figure S7A
Description: Differential relative abundance of bacterial families and genus exhibiting the diet effect. LEfSe analysis identified significantly different taxa between diet-uncontrolled (red, T1Single) and diet-controlled (light blue, T2Single) conditions.
Abundance in Group 1: increased abundance in Controlled diet (T2 single)
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2C and Figure S7A
Description: Differential relative abundance of bacterial families and genus exhibiting the diet effect. LEfSe analysis identified significantly different taxa between diet-uncontrolled (red, T1Single) and diet-controlled (light blue, T2Single) conditions.
Abundance in Group 1: decreased abundance in Controlled diet (T2 single)
Revision editor(s): MyleeeA
