Changes in the vaginal microbiota across a gradient of urbanization/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
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lifestyle measurement Lifestyle measurement,lifestyle measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Amerindians
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mestizos
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 2e
Description: Discriminant taxa analysis between ethnicities; Amerindians and Mestizos (LEfSe).
Abundance in Group 1: increased abundance in Mestizos
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Mobiluncus mulieris |
Revision editor(s): Tosin
Signature 2
Source: Figure 2e
Description: Discriminant taxa analysis between ethnicities; Amerindians and Mestizos (LEfSe).
Abundance in Group 1: decreased abundance in Mestizos
| NCBI | Quality Control | Links |
|---|---|---|
| Peptoniphilus lacrimalis | ||
| Brevibacterium linens |
Revision editor(s): Tosin
