Changes in the vaginal microbiota across a gradient of urbanization
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
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
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
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
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
Signature 1
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 CST-G.vaginalis
| NCBI | Quality Control | Links |
|---|---|---|
| Gardnerella vaginalis |
Revision editor(s): Tosin
Experiment 4
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
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
Signature 1
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 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
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
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
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
Signature 1
Source: Figure S3d
Description: Discriminant taxa analysis within Mestizos by body site.
Abundance in Group 1: increased abundance in Introitus
| NCBI | Quality Control | Links |
|---|---|---|
| anaerococcus christenseniianaerococcus christensenii |
Revision editor(s): Tosin
Experiment 9
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
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
Signature 1
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
Subjects
- 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
- 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
- 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
Signature 1
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
Signature 2
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
Experiment 12
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
- 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
