The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection

Abstract

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.

Keywords: HIV; Human papillomavirus (HPV); Microbiota; Penile.

Fig. 1

Correlogram of 13 bacterial families showing co-occurrence and co-exclusion patterns. These were computed by Spearman’s rank correlation between the families. The correlation coefficients range from − 1 (red; co-exclusions relationships) to + 1 (blue; co-occurrence relationships), hence, high negative and positive coefficient values indicate strong correlations. The blue diagonal line represents correlations of + 1. White shows absence of bacterial relationships

Fig. 2

Community state types (CSTs) identified in the penile microbiota. a) Heatmap of the relative abundances of bacterial taxa in the 238 penile microbiota. Taxa names of bacteria are shown on the left of the heatmap. The “Other” comprised of pooled bacteria at < 0.31% relative abundance each (n = 622, total relative abundance: 6.49%). Rows represent the bacterial taxa and columns the samples. The colour key for the relative abundances is indicated in the upper right corner. The human immunodeficiency virus (HIV), human papillomavirus (HPV) and high-risk human papillomavirus (HR-HPV) infection status of the men are indicated. The dendrogram based on average linkage hierarchical clustering of the Bray-Curtis dissimilarity matrix is shown and was used to define the six community state types (CST-1 through − 6). b) Comparison of the alpha diversity of penile microbiota grouped by individual and pooled CSTs. c) Comparison of beta diversity (UniFrac distance) of the penile microbiota grouped by individual and pooled CSTs

Fig. 3

Alpha diversity measures of penile microbiota. Comparison of the alpha diversity of penile microbiota grouped by a) high-risk human papillomavirus (HR-HPV) infection status, b) human immunodeficiency virus (HIV) infection status, c) HR-HPV and HIV infection status, and d) CD4⁺ T-cell count status. In each plot, the box ranges from the first to the third quartile, with the median represented by the horizontal line. The whiskers extend to the smallest and largest non-outliers and outliers are represented by dots

Fig. 4

Beta diversity of the penile microbiota. Principal Coordinates Analysis (PCoA) plots of the weighted UniFrac distances of the penile microbiota coloured according to a) high-risk human papillomavirus (HR-HPV) infection status, b) human immunodeficiency virus (HIV) infection status, c) HIV and HR-HPV infection, and d) CD4⁺ T-cell count status. The first two principal coordinate axes of variations and the percentage variation explained by each (Axis.1: 45.3% and Axis.2: 14.9% (a-c); and Axis.1: 42.9% and Axis.2: 16.0% (d)) are shown. Each solid point is a bacterial community

Fig. 5

Potential biomarkers for HR-HPV infection by LEfSe. a) Histogram of differentially abundant taxa in penile microbiota of men with and without HR-HPV infections, and b) a six-level cladogram with a taxonomic hierarchical structure indicating differentially abundant taxa in penile microbiota of men with and without HR-HPV infections. Each coloured solid represents a taxon and its diameter is proportional to the taxon’s relative abundance. Blue and green colours represent statistically significant taxon ranks in HR-HPV-positive and negative group, respectively. For visualisation purposes, only differentially abundant features at logarithmic LDA scores > 3.0 or < − 3.0 are shown. Asterisks in the histogram indicate significantly differentially abundant taxa with q < 0.2 after FDR correction

Fig. 6

Potential biomarkers for HIV infection by LEfSe. a) Histogram of differentially abundant taxa in penile microbiota of men with and without human immunodeficiency virus (HIV) infection, and b) a six-level cladogram with a taxonomic hierarchical structure. Each coloured solid represents a taxon and its diameter is proportional to the taxon’s relative abundance. Blue and green solids represent statistically significant taxon ranks in men with and without HIV infection, respectively. Only differentially abundant features at logarithmic LDA scores > 2.0 or < − 2.0 are shown. Asterisks indicate significantly differentially abundant taxa with q < 0.2 after FDR correction