Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques/Experiment 7

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Needs review

Curated date: 2024/04/04

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

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
Complete microbiome social group R
Group 1 name Corresponds to the case (exposed) group for case-control studies
Complete microbiome social group V
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming
Group 0 sample size Number of subjects in the control (unexposed) group
11
Group 1 sample size Number of subjects in the case (exposed) group
12

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

Signature 1

Needs review

Curated date: 2024/04/04

Curator: Fiddyhamma

Revision editor(s): Fiddyhamma

Source: Fig 2B, text

Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.

Abundance in Group 1: decreased abundance in Complete microbiome social group V

NCBI Quality ControlLinks
Actinomycetota

Revision editor(s): Fiddyhamma