Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries
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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
Roachford OSE, Alleyne AT, Nelson KE
Journal
PeerJ
Year
2022
Keywords:
Ancestries, CST subtypes, Community state types, Ethnicity, Gardnerella, Lactobacillus, Mycoplasma, Pathobionts, Prevotella, Vaginal microbiome
BACKGROUND: Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV). The objective of this study was to characterize the vaginal microbiomes across a more diverse intercontinental group of women (N = 151) of different ethnicities (African American, African Kenyan, Afro-Caribbean, Asian Indonesian and Caucasian German) using 16S rRNA gene sequence analysis to determine their structures and offer a comprehensive description of the non-Lactobacillus dominant CSTs and subtypes. RESULTS: In this study, the bacterial composition of the vaginal microbiomes differed significantly among the ethnic groups. Lactobacillus spp. (L. crispatus and L. iners) dominated the vaginal microbiomes in African American women (91.8%) compared to European (German, 42.4%), Asian (Indonesian, 45.0%), African (Kenyan, 34.4%) and Afro-Caribbean (26.1%) women. Expanding on CST classification, three subtypes of CST IV (CST IV-A, IV-B and IV-C) (N = 56, 37.1%) and four additional CSTs were described: CST VI Gardnerella vaginalis-dominant (N = 6, 21.8%); CST VII (Prevotella-dominant, N = 1, 0.66%); CST VIII (N = 9, 5.96%), resembling aerobic vaginitis, was differentiated by a high proportion of taxa such as Enterococcus, Streptococcus and Staphylococcus (relative abundance [RA] > 50%) and CST IX (N = 7, 4.64%) dominated by genera other than Lactobacillus, Gardnerella or Prevotella (e.g., Bifidobacterium breve and Anaerococcus vaginalis). Within the vaginal microbiomes, 32 "taxa with high pathogenic potential" (THPP) were identified. Collectively, THPP (mean RA ~5.24%) negatively correlated (rs = -0.68, p < 2.2e-16) with Lactobacillus species but not significantly with Gardnerella/Prevotella spp. combined (r = -0.13, p = 0.1). However, at the individual level, Mycoplasma hominis exhibited moderate positive correlations with Gardnerella (r = 0.46, p = 2.6e-09) and Prevotella spp. (r = 0.47, p = 1.4e-09). CONCLUSIONS: These findings while supporting the idea that vaginal microbiomes vary with ethnicity, also suggest that CSTs are more wide-ranging and not exclusive to any particular ethnic group. This study offers additional insight into the structure of the vaginal microbiome and contributes to the description and subcategorization of non-Lactobacillus-dominated CSTs.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Subjects
- Location of subjects
- Germany
- Indonesia
- Kenya
- 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
- Mucosa of vagina Mucosa of organ of vagina,Mucous membrane of vagina,Organ mucosa of vagina,Tunica mucosa vaginae,Vagina mucosa,Vagina mucosa of organ,Vagina mucous membrane,Vagina organ mucosa,Vaginal mucosa,Mucosa of vagina,mucosa of vagina
- 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
- Combination of groups - African American (AA), Afro-Caribbean (AC), Asian Indonesian (AI) and African Kenyan (AK) women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Main group - Caucasian German (CG) women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Caucasian German women with varying vaginal microbiome compositions.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 113
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
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
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Source: Figure 3
Description: Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).
Abundance in Group 1: increased abundance in Main group - Caucasian German (CG) women
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium breve | ||
| Gardnerella vaginalis | ||
| Gemella | ||
| Gemelliphila asaccharolytica | ||
| Prevotella amnii | ||
| Veillonella montpellierensis | ||
| family XIfamily XI |
Revision editor(s): Chrisawoke
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of groups - African American (AA), Afro-Caribbean (AC), Asian Indonesian (AI) and Caucasian German (CG) women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- African Kenyan (AK) women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The vaginal microbiome compositions of African Kenyan women descent.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 120
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Source: Figure 3
Description: Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).
Abundance in Group 1: increased abundance in African Kenyan (AK) women
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonadaceae | ||
| Porphyromonas | ||
| Corynebacterium pyruviciproducens |
Revision editor(s): Chrisawoke
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of groups - African American (AA), Afro-Caribbean (AC), Caucasian German (CG) and African Kenyan (AK) women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Asian Indonesian (AI) women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Asian Indonesian women with different vaginal microbiome compositions.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 115
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Source: Figure 3
Description: Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).
Abundance in Group 1: increased abundance in Asian Indonesian (AI) women
Revision editor(s): Chrisawoke
Experiment 4
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of groups - African American (AA), Caucasian German (CG), Asian Indonesian (AI) and African Kenyan (AK) women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Afro-Caribbean (AC) women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vaginal microbiome compositions of Afro-Caribbean women descent.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 133
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Source: Figure 3
Description: Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).
Abundance in Group 1: increased abundance in Afro-Caribbean (AC) women
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus vaginalis | ||
| Bacteroidales | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Hoylesella buccalis | ||
| Peptoniphilus | ||
| Peptoniphilus lacrimalis | ||
| Prevotella | ||
| Prevotella bivia | ||
| Prevotellaceae |
Revision editor(s): Chrisawoke
Experiment 5
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-28
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of groups - Caucasian German (CG), Afro-Caribbean (AC), Asian Indonesian (AI) and African Kenyan (AK) women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- African American (AA) women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- African American women with different vaginal microbiome compositions.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 123
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-25
Source: Figure 3
Description: Linear discriminant analysis plot showing differentiating bacterial taxa of the vaginal microbiomes of the five ethnic groups (AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan and CG, Caucasian German).
Abundance in Group 1: increased abundance in African American (AA) women
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus crispatus |
Revision editor(s): Chrisawoke
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