The penile microbiota of Black South African men: relationship with human papillomavirus and HIV 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, Cozzuto L, Bonnin S, Mbulawa ZZA, Coetzee D, Ponomarenko J, Meiring TL
Journal
BMC microbiology
Year
2020
Keywords:
HIV, Human papillomavirus (HPV), Microbiota, Penile
BACKGROUND: To date, the microbiota of the human penis has been studied mostly in connection with circumcision, HIV risk and female partner bacterial vaginosis (BV). These studies have shown that male circumcision reduces penile anaerobic bacteria, that greater abundance of penile anaerobic bacteria is correlated with increased cytokine levels and greater risk of HIV infection, and that the penile microbiota is an important harbour for BV-associated bacteria. While circumcision has been shown to significantly reduce the risk of acquiring human papillomavirus (HPV) infection, the relationship of the penile microbiota with HPV is still unknown. In this study, we examined the penile microbiota of HPV-infected men as well as the impact of HIV status. RESULTS: The penile skin microbiota of 238 men from Cape Town (South Africa) were profiled using Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene. Corynebacterium and Prevotella were found to be the most abundant genera. Six distinct community state types (CSTs) were identified. CST-1, dominated by Corynebacterium, corresponded to less infections with high-risk HPV (HR-HPV) relative to CSTs 2-6. Men in CST-5 had greater relative abundances of Prevotella, Clostridiales, and Porphyromonas and a lower relative abundance of Corynebacterium. Moreover, they were significantly more likely to have HPV or HR-HPV infections than men in CST-1. Using a machine learning approach, we identified greater relative abundances of the anaerobic BV-associated bacteria (Prevotella, Peptinophilus, and Dialister) and lower relative abundance of Corynebacterium in HR-HPV-infected men compared to HR-HPV-uninfected men. No association was observed between HIV and CST, although the penile microbiota of HIV-infected men had greater relative abundances of Staphylococcus compared to HIV-uninfected men. CONCLUSIONS: We found significant differences in the penile microbiota composition of men with and without HPV and HIV infections. HIV and HR-HPV infections were strongly associated with greater relative abundances of Staphylococcus and BV-associated bacterial taxa (notably Prevotella, Peptinophilus and Dialister), respectively. It is possible that these taxa could increase susceptibility to HIV and HR-HPV acquisition, in addition to creating conditions in which infections persist. Further longitudinal studies are required to establish causal relationships and to determine the extent of the effect.
Experiment 1
Needs review
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
- Skin of penis Penile skin,Penis skin,Penis zone of skin,Zone of skin of penis,Skin of penis,skin of penis
- 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
- High-Risk HPV Negative (HR-HPV Negative)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-Risk HPV Positive (HR-HPV Positive)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High-Risk HPV Positive (HR-HPV Positive) refers to individuals infected with Human Papillomavirus.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 81
- Group 1 sample size Number of subjects in the case (exposed) group
- 102
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
- 3
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Fig. 5
Description: Significant differentially abundant taxa between HR-HPV positive and negative individuals.
Abundance in Group 1: increased abundance in High-Risk HPV Positive (HR-HPV Positive)
| NCBI | Quality Control | Links |
|---|---|---|
| Peptoniphilus | ||
| Dialister | ||
| unclassified Eubacteriales | ||
| Prevotella |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Fig. 5
Description: Significant differentially abundant taxa between HR-HPV positive and negative individuals.
Abundance in Group 1: decreased abundance in High-Risk HPV Positive (HR-HPV Positive)
| NCBI | Quality Control | Links |
|---|---|---|
| Brevibacteriaceae | ||
| Actinomycetales |
Revision editor(s): KateRasheed
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HR-HPV-uninfected in HIV-negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HR-HPV-infected in HIV-negative
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HR-HPV-infected in HIV-negative refers to the presence of High-Risk Human papillomavirus (HPV) in men that are not infected with HIV.
- 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
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Additional file 5: Figure S3
Description: Significant differentially abundant taxa between HR-HPV-infected in HIV-negative and HR-HPV-uninfected in HIV-negative individuals.
Abundance in Group 1: decreased abundance in HR-HPV-infected in HIV-negative
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Brevibacterium | ||
| Brachybacterium |
Revision editor(s): KateRasheed
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human immunodeficiency virus AIDS virus,HIV,Human immunodeficiency virus,human immunodeficiency virus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV - negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV - positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV - positive refers to individuals infected with Human Immunodeficiency Virus.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 150
- Group 1 sample size Number of subjects in the case (exposed) group
- 88
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Fig. 6
Description: Significant differentially abundant taxa between HIV positive and negative individuals.
Abundance in Group 1: decreased abundance in HIV - positive
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Actinomycetales |
Revision editor(s): KateRasheed
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- 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
- Non-Corynebacterium-dominated microbiota (Diverse penile microbiota (CSTs 2-5))
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Corynebacterium-dominated penile microbiota (CST-1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Corynebacterium-dominated penile microbiota (CST-1) refers to men who had less HR-HPV.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 111
- Group 1 sample size Number of subjects in the case (exposed) group
- 127
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Needs review
Source: Additional file 3: Table S2
Description: Differentially abundant taxa in men with Corynebacterium-dominated versus diverse penile microbiota.
Abundance in Group 1: increased abundance in Corynebacterium-dominated penile microbiota (CST-1)
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Additional file 3: Table S2
Description: Differentially abundant taxa in men with Corynebacterium-dominated versus diverse penile microbiota.
Abundance in Group 1: decreased abundance in Corynebacterium-dominated penile microbiota (CST-1)
Revision editor(s): KateRasheed
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