Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Yang L, Hao Y, Hu J, Kelly D, Li H, Brown S, Tasker C, Roche NE, Chang TL, Pei Z
Journal
Emerging microbes & infections
Year
2019
Keywords:
HIV acquisition, Vaginal microbiome, bacterial vaginosis-associated bacteria, depot medroxyprogesterone acetate, network
The use of depot medroxyprogesterone acetate (DMPA), a 3-monthly injectable hormonal contraceptive, is associated with an increased risk of HIV acquisition possibly through alteration of the vaginal microbiome. In this longitudinal interventional study, we investigated the impact of DMPA administration on the vaginal microbiome in Hispanic White and Black women at the baseline (visit 1), 1 month (visit 2), and 3 months (visit 3) following DMPA treatment by using 16S rRNA gene sequencing. No significant changes in the vaginal microbiome were observed after DMPA treatment when Hispanic White and Black women were analysed as a combined group. However, DMPA treatment enriched total vaginosis-associated bacteria (VNAB) and Prevotella at visit 2, and simplified the correlational network in the vaginal microbiome in Black women, while increasing the network size in Hispanic White women. The microbiome in Black women became more diversified and contained more VNAB than Hispanic White women after DMPA treatment. While the Firmicutes to Bacteroidetes (F/B) ratio and Lactobacillus to Prevotella (L/P) ratio were comparable between Black and Hispanic White women at visit 1, both ratios were lower in Black women than in Hispanic White women at visit 2. In conclusion, DMPA treatment altered the community network and enriched VNAB in Black women but not in Hispanic White women. The Lactobacillus deficiency and enrichment of VNAB may contribute to the increased risk of HIV acquisition in Black women. Future studies on the impact of racial differences on the risk of HIV acquisition will offer insights into developing effective strategies for HIV prevention. Abbreviations: DMPA: depot medroxyprogesterone acetate; PCR: polymerase chain reaction; OTU: operational taxonomic unit; STI: sexually transmitted infections; VNAB: vaginosis-associated bacteria.
Experiment 1
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
- depot medroxyprogesterone acetate vaginal microbiome (visit 2) among black participants
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- naive black participants (baseline visit)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- participants who had not yet been given the medroxyprogesterone acetate treatment 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
- 16
- 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
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Source: Figure 1
Description: Differential genera between naive and DMPA-treated vaginal microbiomes in Hispanic White and Black women
Abundance in Group 1: increased abundance in naive black participants (baseline visit)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
Differences from previous experiment shown
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
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
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- black participants after using depot medroxyprogesterone (visit 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- white participants after using depot medroxyprogesterone (visit 2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- white participants at visit 2
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Source: Figure 3
Description: Differential genera between Hispanic White and Black women at visit 2
Abundance in Group 1: increased abundance in white participants after using depot medroxyprogesterone (visit 2)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
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 visit 2
Abundance in Group 1: decreased abundance in white participants after using depot medroxyprogesterone (visit 2)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Fusobacterium | ||
| Gemella | ||
| Prevotella | ||
| Sneathia |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- black participants after using depot medroxyprogesterone (visit 3)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- white participants after using depot medroxyprogesterone (visit 3)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- white participants at visit 3
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
Source: Figure 3
Description: Differentially abundant genera between Hispanic White and Black women at visit 3
Abundance in Group 1: increased abundance in white participants after using depot medroxyprogesterone (visit 3)
| 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: Differentially abundant genera between Hispanic White and Black women at visit 3
Abundance in Group 1: decreased abundance in white participants after using depot medroxyprogesterone (visit 3)
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcus | ||
| Megasphaera | ||
| Prevotella |
Revision editor(s): Claregrieve1, WikiWorks
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