Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-1-16
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 Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Contraception contraceptive management,Contraception,contraception
- 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)
- 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, Confounders controlled for: "condom use" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.condom use
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-16
Source: Table 3A
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 gasseri | ||
| Lactobacillus iners | ||
| Lactobacillus jensenii | ||
| Lactobacillus johnsonii | ||
| Lactobacillus taiwanensis | ||
| Veillonella montpellierensis |
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-16
Source: Table 3A
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
