Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- Venezuela
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Retroarticular Retroarticular,retroarticular
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body composition measurement Body composition measurement,body composition measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- western HMP
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- adult Yanomami
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals from a remote Yanomami community in Venezuela, living a seminomadic hunter-gatherer lifestyle in the Amazon rainforest
- 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
- 5
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- relative abundances
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "body sites" 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.body sites
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 2D
Description: LEfSe analysis showing most differential bacterial species on retroauricular crease (RAC) of adult Yanomami and western HMP
Abundance in Group 1: increased abundance in adult Yanomami
Revision editor(s): Ese
Signature 2
Source: Figure 2D
Description: LEfSe analysis showing most differential bacteria on retroauricular crease (RAC) of adult Yanomami and western HMP
Abundance in Group 1: decreased abundance in adult Yanomami
| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium acnes | ||
| Cutibacterium granulosum | ||
| Cutibacterium namnetense | ||
| Propionibacterium |
Revision editor(s): Ese
