A Hidden Microbiome Inside the Penis Is Altered in Men Who Have Vaginal Sex

Advocates of drinking your own pee look away: not only is urine not sterile, but a new study suggests that a significant proportion of the microbes in the male urethra come from a source outside the body – at least in men who have vaginal sex.

The study was published in Cell Reports Medicine.

Where do genital microbes come from?

The microbiome refers to the community of microbial life – bacteria, fungi and viruses included – that calls our body home. While much attention has been drawn to the role of our gut microbiome in our general health, microbes live everywhere in our bodies, and some populations remain poorly studied.

“We know where bugs in the gut come from; they primarily come from our surroundings through fecal–oral transfer. But where does genital microbiology come from?” says microbiologist David Nelson of Indiana University.

Nelson and colleagues dug out the answer by subjecting 110 (presumably well-compensated) healthy adult male volunteers to urethral swabs. None of the participants had any inflammation in their urethras and participants with sexually transmitted infections (STIs) were screened out of the study. These samples were then sequenced to reveal the microbial populations, which can be separated into two groups – those native to the urethra, and those from a foreign source.

The native population, researchers found, is the core community that supports the health of the urethra. These bacteria were sparsely found and were likely to live close to the urethra’s opening at the end of the penis, where there is a ready supply of oxygen, which they metabolize.

Reshaping the urethral microbiome

But in a proportion of the men, a more complicated second group of bacteria were identified. These bacteria are usually found inside the vagina, where they can cause disturbances to its healthy ecosystem. Thriving in oxygen-poor settings, these bacteria were found deeper in the urethra. Perhaps unsurprisingly, only men who reported having vaginal sex carried these bacteria.

This relationship was a close link. Men who reported only having oral or anal sex did not harbor vaginal bacteria, and it was noted that these external microbial contributions remained in the urethra up to two months after the men’s last reported vaginal sex, suggesting that regular vaginal sex can reshape the male urethral microbiome.

The influence of vaginal sex was so strong that it explained 10% of the variation of the entire urethral microbiome. “The fact that a specific behavior is such a strong determinant is just profound,” Nelson commented.

The researchers now plan to test whether microbes can migrate from the male urethra to the vagina in a similar fashion. By only using men with healthy urethras, the team has been able to create a mark against which future studies of diseased urethras, such as those affected by urinary tract infections, can be measured. “It is important to set this baseline,” says co-senior author Qunfeng Dong, a bioinformatician at Loyola University Chicago. “Only by understanding what health is can we define what diseases are.”

“STIs really impact people who are socioeconomically disadvantaged; they disproportionately impact women and minorities. It’s a part of health care that’s overlooked because of stigma. I think our study has the potential to dramatically change how we handle STI diagnosis and management in a positive way,” Nelson concluded.

Reference: Toh E, Xing Y, Gao X et al. Sexual behavior shapes male genitourinary microbiome composition. Cell Reports Medicine. 2023; 4; 100981. doi: 10.1016/j.xcrm.2023.100981

This article is a rework of a press release issued by Cell Press. Material has been edited for length and content.