Changes in the vaginal microbiota across a gradient of urbanization/Experiment 5
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
- Vaginal microbiome measurement vaginal flora measurement,vaginal microbiota measurement,Vaginal microbiome measurement,vaginal microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of CST-L.iners, CST-div1 and CST-G.vaginalis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Community State Type diverse cluster 2-CST-div2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Community State Type diverse cluster 2-CST-div2 refers to community state type diverse cluster that is associated with highest vaginal pH and alpha diversity
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure 3c
Description: Cervicovaginal microbiota composition and community state type (CST) clustering. Discriminant taxa for CST-div2.
Abundance in Group 1: increased abundance in Community State Type diverse cluster 2-CST-div2
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia sanguinegens | ||
| Sneathia vaginalis | ||
| Prevotella bivia | ||
| Fannyhessea vaginae | ||
| Megasphaera | ||
| Senegalimassilia | ||
| Clostridium | ||
| Parvimonas micra |
Revision editor(s): Tosin
