Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- United States of America
- 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 Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- 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
- BV-Negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BV-Positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- BV is a type of vaginal inflammation caused by bacterial overgrowth that upsets the healthy microbiome of the vagina, which often leads to elevated vaginal pH and symptoms of abnormal discharge and odor.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- 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
- V3-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).
- relative abundances
- Statistical test
- ANCOM-BC
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- 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
- 1
Signature 1
Source: Figures 4A and 4B
Description: Differential abundance (DA) analysis and modularized co-occurrence network analysis of BV-POS and BV-NEG samples.
Abundance in Group 1: increased abundance in BV-Positive
Revision editor(s): Miss Lulu
Signature 2
Source: Figure 4A
Description: Differential abundance (DA) analysis and modularized co-occurrence network analysis of BV-POS and BV-NEG samples.
Abundance in Group 1: decreased abundance in BV-Positive
Revision editor(s): Miss Lulu