Clinical Significance of Composition and Functional Diversity of the Vaginal Microbiome in Recurrent Vaginitis/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- South Korea
- 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
- Posterior fornix of vagina Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Vaginitis inflammation of vagina,vagina inflammation,vaginal Inflammation,vaginal inflammation,vaginitis,vaginitis (disease),Vaginitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy women (control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Recurrent vaginitis (RV)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women of reproductive age diagnosed with Recurrent vaginitis (RV).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: FIG 5 (A)
Description: Differential abundance of the bacterial taxa in three CST (I, III, and IV) groups of vaginal samples of patients with RV (A) Linear discriminant analysis (LDA) effect size (LEfSe) analysis indicating significant differences in bacterial taxa (LDA score > 2.0; p < 0.05).
Abundance in Group 1: increased abundance in Recurrent vaginitis (RV)
Revision editor(s): Rahila
