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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
- Lifestyle measurement Lifestyle measurement,lifestyle measurement
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "urbanization" 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.urbanization, 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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Differences from previous experiment shown
Subjects
- 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 Community State Types(CST-G.vaginalis, CST-div2 and CST-div1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Community State Type- Lactobacillus iners(CST-L. Iners)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Community State Type- Lactobacillus iners(CST-L. Iners) refers to the community state type that is dominated by Lactobacillus iners and associated with lowest vaginal pH and alpha diversity.
- 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
- 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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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 Community State Type- Lactobacillus iners(CST-L. Iners)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Tosin
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
- Community State Type- Gardnerella vaginalis(CST-G.vaginalis)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Community State Type- Gardnerella vaginalis(CST-G.vaginalis) refers to the community state type that is dominated by Gardnerella vaginalis and associated with intermediate alpha diversity; and two highly diverse clusters.
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure 3c
Description: Cervicovaginal microbiota composition and community state type (CST) clustering. Discriminant taxa for CST-G.vaginalis.
Abundance in Group 1: increased abundance in Community State Type- Gardnerella vaginalis(CST-G.vaginalis)
| NCBI | Quality Control | Links |
|---|---|---|
| Gardnerella vaginalis |
Revision editor(s): Tosin
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
- Community State Type diverse cluster 1-CST-div1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Community State Type diverse cluster 1-CST-div1 refers to community state type diverse cluster that is associated with highest vaginal pH and alpha diversity
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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 Community State Type diverse cluster 1-CST-div1
Revision editor(s): Tosin
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
- Community State Type diverse cluster 2-CST-div2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Community State Type diverse cluster 2-CST-div2 refers to community state type diverse cluster that is associated with highest vaginal pH and alpha diversity
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure 3c
Description: Cervicovaginal microbiota composition and community state type (CST) clustering. Discriminant taxa for CST-div2.
Abundance in Group 1: increased abundance in Community State Type diverse cluster 2-CST-div2
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia sanguinegens | ||
| Sneathia vaginalis | ||
| Prevotella bivia | ||
| Fannyhessea vaginae | ||
| Megasphaera | ||
| Senegalimassilia | ||
| Clostridium | ||
| Parvimonas micra |
Revision editor(s): Tosin
Experiment 6
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
- Community State Type diverse cluster 3-CST-div3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Community State Type diverse cluster 3-CST-div3 refers to community state type diverse cluster that has a high diversity and low pH. It was found in the introital sample.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure S3b
Description: Discriminant taxa analysis for initroital CSTs according to LeFSe.
Abundance in Group 1: increased abundance in Community State Type diverse cluster 3-CST-div3
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure S3b
Description: Discriminant taxa analysis for introital CST according to LEFse.
Abundance in Group 1: decreased abundance in Community State Type diverse cluster 3-CST-div3
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Tosin
Experiment 7
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure S3d
Description: Discriminant taxa analysis within Mestizos by body site.
Abundance in Group 1: increased abundance in Introitus
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcus christensenii |
Revision editor(s): Tosin, Svetlana up
Experiment 9
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease,Human papilloma virus infection
- 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
- Positive refers to women with Human Papillomavirus infection(HPV infection).
- 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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
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.
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Figure S4c
Description: Discriminant taxa analysis by HPV status showing a significance in women infected with high-risk HPV.
Abundance in Group 1: increased abundance in Only high risk HPV Type
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella amnii |
Revision editor(s): Tosin
Experiment 11
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lifestyle measurement Lifestyle measurement,lifestyle measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Low and Medium Amerindian urbanization group
- 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
- High Amerindian urbanization group refers to Amerindians living in the high urban areas.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
- Statistical test
- Fisher's Exact Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "village" 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.village
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Low, Medium and High Amerindian urbanization groups.
Abundance in Group 1: increased abundance in High Amerindian urbanization group
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister micraerophilus | ||
| Parvimonas micra | ||
| Sneathia sanguinegens | ||
| Ureaplasma urealyticum |
Revision editor(s): Tosin, KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Low, Medium and High Amerindian urbanization groups.
Abundance in Group 1: decreased abundance in High Amerindian urbanization group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Tosin, KateRasheed
Experiment 13
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Amerindian urbanization group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium Amerindian urbanization group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Medium Amerindian urbanization group refers to Amerindians living in the medium urban areas.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Low and Medium Amerindian urbanization groups.
Abundance in Group 1: decreased abundance in Medium Amerindian urbanization group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners | ||
| Parvimonas micra | ||
| Sneathia sanguinegens | ||
| Ureaplasma urealyticum |
Revision editor(s): KateRasheed
Experiment 14
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Low and High Amerindian urbanization group
- 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
- Mestizos refers to 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
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "urbanization" 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.urbanization, 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Low, High Amerindian urbanization groups and Mestizos.
Abundance in Group 1: increased abundance in Mestizos
| NCBI | Quality Control | Links |
|---|---|---|
| Mobiluncus mulieris |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Low, High Amerindian urbanization groups and Mestizos.
Abundance in Group 1: decreased abundance in Mestizos
| NCBI | Quality Control | Links |
|---|---|---|
| Brevibacterium linens | ||
| Peptoniphilus lacrimalis |
Revision editor(s): KateRasheed
Experiment 15
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Medium Amerindian urbanization group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Medium Amerindian urbanization groups and Mestizos.
Abundance in Group 1: increased abundance in Mestizos
| NCBI | Quality Control | Links |
|---|---|---|
| Peptoniphilus lacrimalis | ||
| Mobiluncus mulieris |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Medium Amerindian urbanization groups and Mestizos.
Abundance in Group 1: decreased abundance in Mestizos
| NCBI | Quality Control | Links |
|---|---|---|
| Brevibacterium linens |
Revision editor(s): KateRasheed
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