Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection

Abstract

Background: The microbiome of the male urogenital tract is poorly described but it has been suggested that bacterial colonization of the male urethra might impact risk of sexually transmitted infection (STI). Previous cultivation-dependent studies showed that a variety of non-pathogenic bacteria colonize the urethra but did not thoroughly characterize these microbiomes or establish links between the compositions of urethral microbiomes and STI.

Methodology/findings: Here, we used 16S rRNA PCR and sequencing to identify bacteria in urine specimens collected from men who lacked symptoms of urethral inflammation but who differed in status for STI. All of the urine samples contained multiple bacterial genera and many contained taxa that colonize the human vagina. Uncultivated bacteria associated with female genital tract pathology were abundant in specimens from men who had STI.

Conclusions: Urine microbiomes from men with STI were dominated by fastidious, anaerobic and uncultivated bacteria. The same taxa were rare in STI negative individuals. Our findings suggest that the composition of male urine microbiomes is related to STI.

Figure 1. Inter-subject variability in 16S rRNA clones in urine.

4,386-16S rRNA Urine sequences were sorted to the Phyla level using RDP Classifier at 90% confidence cutoff . Subjects are indicated below bars on the X-axis and the percents of clones corresponding to specific phyla are indicated on the Y-axis. STI status of the subjects is indicated below the X-axis.

Figure 2. Hierarchical clustering of urine microbiomes.

Genus names corresponding to terminal taxa depicted in the heat map are listed to the right of the figure. Subjects are listed at the bottom. Intensity of the coloration of cells in the heat map indicates the extent of correlation of different urine samples. Dendograms at the top and right of the heat map indicate relationships of microbiomes and genera, respectively. The top infection color bar indicates STI (labeled as YES) or non-STI (labeled as NONE) participants.

Figure 3. Unifrac community comparison of urine.

Clustering of urine microbiomes was performed using un-weighted Unifrac . The percent variations explained by each principle component are indicated on the axis. Blue circles indicate urine from individuals positive for STI; red circles correspond to urine negative for STI.