The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels/Experiment 10

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Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/03/25

Curator: Joan Chuks

Revision editor(s): Joan Chuks, Ikehdarlington, 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

Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Infant macaques

Group 1 name Corresponds to the case (exposed) group for case-control studies

Juvenile macaques

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Assamese macaques aged 4–5 years

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

7

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

increased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

increased