Sexual behavior shapes the adult male genitourinary microbiome

The origins, composition, and significance of the microbiome of the distal penile urethra, the combined entrance to the male reproductive and urinary tracts, is unknown. In contrast, vaginal microbiome composition is a key genitourinary infection risk determinant in women, and development of less-protective dysbiotic vaginal microbiomes is linked to sexual exposures. Here, we characterized the urethral microbiome in 110 men who did not have STIs, urethral inflammation, or genitourinary symptoms using shotgun metagenomics. Lactic acid bacteria and Corynebacteria spp. were detected in most of the urethral specimens, suggesting that these organisms constitute a core urethral microbiome in adult men. However, some specimens also contained high loads of bacterial vaginosis and aerobic vaginitis associated bacteria, and these bacteria were only detected in specimens from men who reported vaginal intercourse. Sexual behavior in some intervals explained over 10% of the total variance in urethral microbiome composition. In contrast, none of the other demographic, behavioral, or clinical factors captured were associated with urethral microbiome composition. Thus, the adult male urethra supports a characteristic core microbiome that can be dramatically re-shaped by sexual behavior, and an array of sexually transmitted microorganisms can silently colonize the male urethra, likely to promote their dispersal via vaginal intercourse.