Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- South Africa
- 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
- NET-En (norethisterone enanthate ) arm
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- COC (combined oral contraceptives) arm
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (adolescents) who were randomized to combined oral contraceptives.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Past 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- raw counts
- Statistical test
- DESeq2
- 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)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Table 3
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover [COC (combined oral contraceptives) vs Net EN (norethisterone enanthate) arm].
Abundance in Group 1: increased abundance in COC (combined oral contraceptives) arm
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners | ||
| Lactobacillus jensenii | ||
| Veillonella montpellierensis | ||
| Lactobacillus johnsonii | ||
| Lactobacillus gasseri | ||
| Lactobacillus taiwanensis |
Revision editor(s): Tosin
Signature 2
Source: Table 3
Description: DESeq2 analysis of taxa differentially abundant between randomized study arms at crossover COC (combined oral contraceptives) vs Net EN (norethisterone enanthate ) arm].
Abundance in Group 1: decreased abundance in COC (combined oral contraceptives) arm
Revision editor(s): Tosin
