Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques/Experiment 3

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Curated date: 2024/04/03

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma, Victoria

Subjects

Location of subjects

United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.

Macaca mulatta

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Axilla skin Axillary skin,Skin of axilla,Axilla skin,axilla skin

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Microbiome measurement Microbiome measurement,microbiome measurement

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

Core microbiome social groups (V)

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

Core microbiome social groups (F)

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

The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features.

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

Mann-Whitney (Wilcoxon)

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: "sampling period" 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.sampling period

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

increased