The effects of circumcision on the penis microbiome

Abstract

Background: Circumcision is associated with significant reductions in HIV, HSV-2 and HPV infections among men and significant reductions in bacterial vaginosis among their female partners.

Methodology/principal findings: We assessed the penile (coronal sulci) microbiota in 12 HIV-negative Ugandan men before and after circumcision. Microbiota were characterized using sequence-tagged 16S rRNA gene pyrosequencing targeting the V3-V4 hypervariable regions. Taxonomic classification was performed using the RDP Naïve Bayesian Classifier. Among the 42 unique bacterial families identified, Pseudomonadaceae and Oxalobactericeae were the most abundant irrespective of circumcision status. Circumcision was associated with a significant change in the overall microbiota (PerMANOVA p = 0.007) and with a significant decrease in putative anaerobic bacterial families (Wilcoxon Signed-Rank test p = 0.014). Specifically, two families-Clostridiales Family XI (p = 0.006) and Prevotellaceae (p = 0.006)-were uniquely abundant before circumcision. Within these families we identified a number of anaerobic genera previously associated with bacterial vaginosis including: Anaerococcus spp., Finegoldia spp., Peptoniphilus spp., and Prevotella spp.

Conclusions/significance: The anoxic microenvironment of the subpreputial space may support pro-inflammatory anaerobes that can activate Langerhans cells to present HIV to CD4 cells in draining lymph nodes. Thus, the reduction in putative anaerobic bacteria after circumcision may play a role in protection from HIV and other sexually transmitted diseases.

Figure 1. Heatmap display of the bacterial families in the coronal sulci microbiota pre- and post-circumcision.

The microbiota from 12 paired coronal sulci samples is presented with the abundance of each phylotype represented by a colored block as specified in the legend.

Figure 2. Shannon-Weaver diversity indices generated using the 16S rRNA gene pyrosequencing data.

The diversity index is based on the number of unique phylotypes and their frequency, with the rare phylotypes having lower effect on the diversity index. These analyses indicate that diversity was sufficiently described after analyzing 387 sequences from each sample. Pre-circumcision samples appeared to have a greater range of community diversity as compared to post-circumcision. Solid lines = pre-circumcision; dotted line = post-circumcision.

Figure 3. Comparison of pre- and post-circumcision coronal sulci microbiota using nMDS ordination.

nMDS is an ordination method that ranks the distances calculated using community data, with each data point representing the community data from a single sample; it is used to reduce data complexity and to extract meaningful relationships amongst communities. Lines connect individual communities to the centroid values for each group.