Changes in the vaginal microbiota across a gradient of urbanization/Experiment 6
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
- CST-L.iners
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Community State Type diverse cluster 3-CST-div3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Community State Type diverse cluster 3-CST-div3 refers to community state type diverse cluster that has a high diversity and low pH. It was found in the introital sample.
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure S3b
Description: Discriminant taxa analysis for initroital CSTs according to LeFSe.
Abundance in Group 1: increased abundance in Community State Type diverse cluster 3-CST-div3
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure S3b
Description: Discriminant taxa analysis for introital CST according to LEFse.
Abundance in Group 1: decreased abundance in Community State Type diverse cluster 3-CST-div3
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Tosin
