Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
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 Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Medroxyprogesterone acetate (6alpha)-6-methyl-3,20-dioxopregn-4-en-17-yl acetate,Medroxyprogesterone acetate,medroxyprogesterone acetate
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- black naive vaginal microbiome (baseline visit )
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- white naiive vaginal microbiome (baseline)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- white participants at baseline
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- before sample collection
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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Source: Figure 3
Description: Differential genera between Hispanic White and Black women at baseline
Abundance in Group 1: increased abundance in white naiive vaginal microbiome (baseline)
| NCBI | Quality Control | Links |
|---|---|---|
| Finegoldia |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Source: Figure 3
Description: Differential genera between Hispanic White and Black women at baseline
Abundance in Group 1: decreased abundance in white naiive vaginal microbiome (baseline)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Shuttleworthella |
Revision editor(s): Claregrieve1, WikiWorks
