Changes in the vaginal microbiota across a gradient of urbanization
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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
Vargas-Robles D, Morales N, Rodríguez I, Nieves T, Godoy-Vitorino F, Alcaraz LD, Pérez ME, Ravel J, Forney LJ, Domínguez-Bello MG
Journal
Scientific reports
Year
2020
The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations. Among these, lifestyle associated with certain sexual and antimicrobial practices may be associated with higher diversity. To test this hypothesis, we characterized the vaginal microbiota in the cervicovaginal and introital sites in sexually active Amerindians (N = 82) spanning urbanization, and in urban mestizos (N = 29), in the Venezuelan Amazonas. HPV status was also considered. Sampling was performed in an urban gradient from remote villages to a town, and women were individually classified by the degree of urbanization (low, medium, and high). Amerindian cervicovaginal and introital microbiota diversity were not associated with major changes in urbanization or ethnicity. There was a non-significant trend of increased diversity with urbanization, with a few taxa found overrepresented in urban Amerindians (Brevibacterium linens and Peptoniphilus lacrimalis) or mestizos (Mobiluncus mulieris and Prevotella sp.). Among all women, cervicovaginal and introital samples clustered, respectively, in four and two community state types (CSTs), where most profiles were dominated by Lactobacillus iners, Gardnerella vaginalis or were highly diverse profiles. HPV status did not associate with microbial diversity. In conclusion, no association was found between urban level and the vaginal microbiome in Amerindian women, and little difference was found between ethnicities. L. iners and high diversity profiles, associated with vaginal health outcomes, prevail in these populations.
Experiment 1
Subjects
- Location of subjects
- Venezuela
- 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
- Human papillomavirus Human Papilloma Virus,human papillomavirus HPV,Human papillomavirus,human papillomavirus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Amerindians
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mestizos
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- ethnic group, Confounders controlled for: "location" 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.location
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 2e
Description: Discriminant taxa analysis between ethnicities; Amerindians and Mestizos (LEfSe).
Abundance in Group 1: increased abundance in Mestizos
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Mobiluncus mulieris |
Revision editor(s): Tosin
Signature 2
Source: Figure 2e
Description: Discriminant taxa analysis between ethnicities; Amerindians and Mestizos (LEfSe).
Abundance in Group 1: decreased abundance in Mestizos
| NCBI | Quality Control | Links |
|---|---|---|
| Peptoniphilus lacrimalis | ||
| Brevibacterium linens |
Revision editor(s): Tosin
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of CST-G.vaginalis, CST-div2 and CST-div1.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CST-L. Iners
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3c
Description: Cervicovaginal microbiota composition and community state type (CST) clustering. Discriminant taxa for CST-L.iners
Abundance in Group 1: increased abundance in CST-L. Iners
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Tosin
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of CST-L.iners, CST-div2 and CST-div1.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CST-G.vaginalis
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of CST-L.iners, CST-div2 and CST-G.vaginalis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CST-div1
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3c
Description: Cervicovaginal microbiota composition and community state type (CST) clustering. Discriminant taxa for CST-div1.
Abundance in Group 1: increased abundance in CST-div1
Revision editor(s): Tosin
Experiment 5
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of CST-L.iners, CST-div1 and CST-G.vaginalis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CST-div2
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Experiment 6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CST-L.iners
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CST-div3
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure S3b
Description: Discriminant taxa analysis for initroital CSTs according to LeFSe.
Abundance in Group 1: increased abundance in CST-div3
Revision editor(s): Tosin
Signature 2
Source: Figure S3b
Description: Discriminant taxa analysis for introital CST according to LEFse.
Abundance in Group 1: decreased abundance in CST-div3
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Tosin
Experiment 7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cervicovaginal
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Introitus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Introitus as vaginal sites for Amerindians.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 95
- Group 1 sample size Number of subjects in the case (exposed) group
- 73
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Fig S3d
Description: Discriminant taxa analysis within Amerinidians by body site.
Abundance in Group 1: decreased abundance in Introitus
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister micraerophilus | ||
| Ureaplasma parvum |
Revision editor(s): Tosin
Experiment 8
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Introitus as vaginal site for Mestizos.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Experiment 9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV positive Status of women.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure S4b
Description: Discriminant taxa analysis by HPV status showing significance in only HPV negative women
Abundance in Group 1: decreased abundance in Positive
| NCBI | Quality Control | Links |
|---|---|---|
| Coriobacteriaceae | ||
| Anaerococcus tetradius |
Revision editor(s): Tosin
Experiment 10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Only low-risk, both risk-types and Negative HPV type
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Only high risk HPV Type
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women that have high risk of HPV.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Experiment 11
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Amerindians
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Amerindian urbanization group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
- Statistical test
- Fisher's Exact Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- ethnic group, Confounders controlled for: "location" 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.location
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