The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels/Experiment 7
Curated date: 2024/03/25
Curator: Ikehdarlington
Revision editor(s): Ikehdarlington, Joan Chuks, Victoria
Subjects
- Location of subjects
- Thailand
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Macaca assamensis
- 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 glucocorticoid response to glucocorticoid stimulus,Response to glucocorticoid,response to glucocorticoid
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Offspring glucocorticoid (OffspringGC) in 4.7 years old (mean age)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Offspring glucocorticoid (OffspringGC) in 2.3 years old (mean age -1SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Assamese macaques aged 2.3 years (equivalent to infant age class), who were affected by increased Offspring Glucocorticoid level (OffspringGC) during the Rich season (periods of abundant food availability)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
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).
- centered log-ratio
- Statistical test
- ANCOM
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 5
Description: Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed during the rich season.
Abundance in Group 1: increased abundance in Offspring glucocorticoid (OffspringGC) in 2.3 years old (mean age -1SD)
Revision editor(s): Ikehdarlington, Joan Chuks
Signature 2
Source: Figure 5
Description: Bacteria Taxa affected by Offspring glucocorticoid (OffspringGC) and determined by ANCOM-BC to be differentially abundant in 2.3 years old Assamese macaques (mean age -1SD, equivalent to infant age class) Versus 4.7 years old Assamese macaques (mean age, equivalent to Juvenile age class) as assessed during the rich season.
Abundance in Group 1: decreased abundance in Offspring glucocorticoid (OffspringGC) in 2.3 years old (mean age -1SD)
Revision editor(s): Ikehdarlington, Joan Chuks
