Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22
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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

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 ControlLinks
Prevotella

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-22

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Finegoldia

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Clostridium
Shuttleworthella

Revision editor(s): Claregrieve1, WikiWorks

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Lactobacillus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Clostridium
Fusobacterium
Gemella
Prevotella
Sneathia

Revision editor(s): Claregrieve1, WikiWorks

Experiment 4


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Finegoldia

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Aerococcus
Megasphaera
Prevotella

Revision editor(s): Claregrieve1, WikiWorks