Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population
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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
Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG, Blaser MJ
Journal
Frontiers in microbiology
Year
2018
Keywords:
16S rRNA, ITS2, cervical cancer, cervicovaginal microbiota, fungi
The human cervicovaginal microbiota resides at an interface between the host and the environment and may affect susceptibility to disease. Puerto Rican women have high human papillomavirus (HPV) infection and cervical cancer rates. We hypothesized that the population structure of the cervicovaginal bacterial and fungal biota changed with cervical squamous intraepithelial lesions and HPV infections. DNA was extracted from cervix, introitus, and anal sites of 62 patients attending high-risk San Juan clinics. The 16S rRNA V4 region and ITS-2 fungal regions were amplified and sequenced using Illumina technology. HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. HPV prevalence was 84% of which ∼44% subjects were infected with high-risk HPV, ∼35% were co-infected with as many as 9 HPV types and ∼5% were infected with exclusively low-risk HPV types. HPV diversity did not change with cervical dysplasia. Cervical bacteria were more diverse in patients with CIN3 pre-cancerous lesions. We found enrichment of Atopobium vaginae and Gardnerella vaginalis in patients with CIN3 lesions. We found no significant bacterial biomarkers associated with HPV infections. Fungal diversity was significantly higher in cervical samples with high-risk HPV and introitus samples of patients with Atypical Squamous Cells of Undetermined Significance (ASCUS). Fungal biomarker signatures for vagina and cervix include Sporidiobolaceae and Sacharomyces for ASCUS, and Malassezia for high-risk HPV infections. Our combined data suggests that specific cervicovaginal bacterial and fungal populations are related to the host epithelial microenvironment, and could play roles in cervical dysplasia.
Experiment 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
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 Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical glandular intraepithelial neoplasia Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Atypical Squamous Cells of Undetermined Significance
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Grade Squamous Intraepithelial Lesion
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- low grade squamous intraepithelial lesion
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- -V2
- 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)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 8
Description: Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in the 58 introitus samples)
Abundance in Group 1: decreased abundance in Low Grade Squamous Intraepithelial Lesion
| NCBI | Quality Control | Links |
|---|---|---|
| Saccharomyces | ||
| Sporidiobolaceae |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by Fatima on 2021/04/20
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low risk-HPV
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High risk-HPV
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High risk-HPV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 8
Description: Fungal biomarker signatures in high risk-HPV group compared to low risk-HPV group (in the 58 introitus samples)
Abundance in Group 1: increased abundance in High risk-HPV
| NCBI | Quality Control | Links |
|---|---|---|
| Malassezia |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Needs review
Source: Figure 8
Description: Fungal biomarker signatures in high risk-HPV group compared to low risk-HPV group (in the 58 introitus samples)
Abundance in Group 1: decreased abundance in High risk-HPV
| NCBI | Quality Control | Links |
|---|---|---|
| Sporidiobolaceae |
Revision editor(s): WikiWorks, ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Uterine cervix
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Atypical Squamous Cells of Undetermined Significance
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Grade Squamous Intraepithelial Lesion
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- low grade squamus intraepithelial lesion
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 8
Description: Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in the 55 cervical samples)
Abundance in Group 1: decreased abundance in Low Grade Squamous Intraepithelial Lesion
| NCBI | Quality Control | Links |
|---|---|---|
| Sporidiobolaceae |
Revision editor(s): ChiomaBlessing, WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low risk-HPV
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High risk-HPV
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High risk-HPV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 8
Description: Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in 55 cervical samples)
Abundance in Group 1: increased abundance in High risk-HPV
| NCBI | Quality Control | Links |
|---|---|---|
| Malassezia |
Revision editor(s): WikiWorks, ChiomaBlessing
Signature 2
Needs review
Source: Figure 8
Description: Fungal biomarker signatures in Low Grade Squamous Intraepithelial Lesion compared to Atypical Squamous Cells of Undetermined Significance (in 55 cervical samples)
Abundance in Group 1: decreased abundance in High risk-HPV
| NCBI | Quality Control | Links |
|---|---|---|
| Sporidiobolaceae |
Revision editor(s): WikiWorks, ChiomaBlessing
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