The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection
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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
Onywera H, Williamson AL, Mbulawa ZZA, Coetzee D, Meiring TL
Journal
Papillomavirus research (Amsterdam, Netherlands)
Year
2019
Keywords:
African, Cervical microbiota, High-risk HPV (HR-HPV), Potential biomarkers, Reproductive-age
In this study we examined potential associations of HPV infection with the cervical microbiota. Cervical samples were collected from 87 HIV-seronegative reproductive-age Black South African women. Microbiota were characterized by Illumina sequencing of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. Thirty seven (42.5%) and 30 (34.5%) of the women had prevalent HPV and high-risk (HR)-HPV, respectively. Only 23 women (26.4%) had cervical microbiota dominated by a single Lactobacillus species (L. crispatus (2/87 (2.3%)), L. jensenii (2/87 (2.3%)), and L. iners (19/87 (21.8%)). The majority of the women (56/87 (64.4%)) had diverse cervical microbiota consisting of mainly bacterial vaginosis-associated bacteria. The remaining women (8/87 (9.2%)) had microbiota dominated by Aerococcus, Streptococcus, Chlamydia or Corynebacterium. Women with HR-HPV had significantly higher relative abundances of Aerococcaceae, Pseudomonadaceae and Bifidobacteriaceae compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05, q < 0.2). Gardnerella, Sneathia, and Atopobium were also found at greater relative abundances in HR-HPV-infected women compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05), although the difference was not significant after FDR-adjustment (q > 0.2). Further investigations of the bacterial taxa significantly enriched in HR-HPV-infected women are warranted.
Experiment 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Subjects
- Location of subjects
- South Africa
- 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
- Uterine cervix Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix
- 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
- 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 infection confirmed through HPV genotyping test
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
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)
- 0.2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: figure 4
Description: Potential biomarkers for high-risk HPV by LefSe
Abundance in Group 1: increased abundance in high risk hpv
| NCBI | Quality Control | Links |
|---|---|---|
| Azotobacter group | ||
| Aerococcaceae | ||
| Coriobacteriales | ||
| Coriobacterium | ||
| Actinomycetota | ||
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Fusobacteriales | ||
| Fusobacteriota |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: figure 4
Description: Potential biomarkers for high-risk HPV by LefSe
Abundance in Group 1: decreased abundance in high risk hpv
| NCBI | Quality Control | Links |
|---|---|---|
| Pasteurellales | ||
| Pasteurellaceae | ||
| Haemophilus | ||
| Alphaproteobacteria | ||
| Gammaproteobacteria | ||
| Pseudomonadales | ||
| Phyllobacterium | ||
| Hyphomicrobiales | ||
| Phyllobacteriaceae |
Revision editor(s): WikiWorks
Experiment 2
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
- no HPV
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV infection confirmed through HPV genotyping test
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 37
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: supplemental figure 2
Description: Potential biomarkers for HPV by LefSe.
Abundance in Group 1: increased abundance in HPV
| NCBI | Quality Control | Links |
|---|---|---|
| Alphaproteobacteria | ||
| Rickettsiales | ||
| Actinomycetes | ||
| Bifidobacteriales | ||
| Bifidobacteriaceae | ||
| Gardnerella |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: supplemental figure 2
Description: Potential biomarkers for HPV by LefSe.
Abundance in Group 1: decreased abundance in HPV
Revision editor(s): WikiWorks
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