Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques/Experiment 4

Needs review

Curated date: 2024/04/04

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

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: Non-Core microbiome 2013 sampling period

Group 1 name Corresponds to the case (exposed) group for case-control studies: Non-Core microbiome 2015 sampling period

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. The same core features were then removed from the complete microbiome table to output a “non-core” microbiome feature table. Core and non-core feature tables were then exported to biom format

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: centered log-ratio

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

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