Parsing the Penis Microbiome

Circumcision and sexual activity are but two factors that can influence the bacterial communities that inhabit male genitalia.

By Tracy Vence | May 29, 2014


Much like the vaginal microbiome differs among women and changes over time, the penis is home to a variety of bacteria that vary with a man’s age, sexual activities, and whether he is circumcised, among other things. And it’s not just the skin that envelops the male sexual organ that’s inhabited by microbes: researchers continue to identify bacteria that dwell within the urogenital tract, a site once considered sterile in the absence of infection.

David Nelson, an associate professor of microbiology and immunology at Indiana University in Bloomington, was investigating Chlamydia infections when he and his colleagues found evidence to suggest that the sexually transmitted pathogens in the urogenital tract were obtaining metabolites from other microbes. “There was a signature in the chlamydial genome that suggested this organism might be interacting with other microorganisms,” said Nelson. “That’s what initially piqued our interest. And when we went in and started to look, we found that there were a lot more [microbes] than we would have anticipated being there.”

The researchers found that some men pass urine containing a variety of lactobacilli and streptococci species, whereas others have more anaerobes, like Prevotella and Fusobacterium. In terms of overall composition, “we see a lot of parallels to the gut,” said Nelson, noting that there doesn’t seem to be a standout formula for a “healthy” urogenital tract. Commensal microbes within the urethra could make a man more susceptible to infection by supporting colonization by pathogens like Chlamydia, whereas bacteria that consume the environment’s nutrients could help prevent it. “We just don’t know at this point,” said Nelson.

“The penis is understudied,” agreed Deborah Anderson, a professor of obstetrics, gynecology, and microbiology at the Boston University School of Medicine. “There could be a very interesting story there, but we haven’t really done the proper research.”

Cutting away bacteria

To date, circumcision is the known largest influence on the composition of the penis microbiome. In a 2010 PLOS ONE paper, Lance Price of the Translational Genomics Research Institute in Phoenix, Arizona, and his colleagues showed that the bacteria that colonized the base of the penis’s tip, or glans, varied before and after circumcision. More specifically, the researchers found fewer anaerobic bacteria within six months after the men in a study were circumcised. Last April, the team confirmed its finding in a larger cohort and published the results in mBio. “It really appears that [the penis microbiome] depends really on whether you’re circumcised or uncircumcised—different organisms dominate,” said Price.

“Men who are uncircumcised have significantly more bacteria on their penis, and the types of bacteria are also very different,” explained Price’s collaborator Cindy Liu, a research pathologist at Johns Hopkins Medicine in Baltimore. “They have a number of different anaerobic species.”

The implications of these findings for men’s health, however, remain unclear. Because such microbes have been implicated in the spread of HIV and other sexually transmitted diseases, the researchers suggested that circumcision might help curb infections, although this has yet to be shown.

Sharing species?

Some of the anaerobes commonly found on the uncircumcised penis and on occasion inside the male urogenital tract are the same species associated with bacterial vaginosis (BV) in women, said Liu, lending support to the idea that male and female sexual partners share genital microbiota.

“Cindy [Liu]’s finding that uncircumcised men had more of these BV bugs is consistent with the epidemiologic investigation that showed that the partners of men who are circumcised have less BV,” said Price.

Anderson and her colleagues have found similar results. “One hypothesis is that the male microbiome might reflect or be related to [his] partner’s microbiome,” she said.

Because sex appears to play a key role in the composition of the penis microbiome, researchers hope to sample men of all ages and with diverse patterns of sexual activity, including those who are not yet sexually active. One challenge to such research, however, is “getting consent of people prior to initiation of sexual activity,” said Nelson.

Another challenge is how few bacteria can be found in some samples. “As compared with the GI tract or the mouth or the vagina, there’s much less bacteria [in and on the penis], so what we’ve had to do is modify our methods to maximize DNA isolation while minimizing contamination,” said Price.

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May 29, 2014

from a clinical perspective, i have found that most forms of balano-posthitis ((inflammation of the glans and foreskin/prepuce) presenting at the clinic heal better and quicker in men who accept as part of the treatment package for the particular inflammation/infection,an incidental circumcision.

; be this the balanoposthitis driven by the glycosuria in uncontrolled diabetes, or the glans ulcers associated with herpes, or the papillomatous eruptions from viral warts.

eradicating the largely anaerobic moistured atmosphere beneath the foreskin with a circumcision seems to wipe out a whole category of pathogens either triggering solo infections or symbiotically facilitating other pathogens or colonisers in and around the penis.


Some studies have sugested that the prepuce may harbour the receptors for the hiv virus and circumcision may be a good means to deny the virus a foothold.

Avatar of: Dan Bollinger

Dan Bollinger

Posts: 1

May 30, 2014

We know from this and other studies that the prepuce (foreskin) physically creates the biome that houses a wide variety of flora, some of which are beneficial to men’s health. We also know that females have a vulvar biome. It is logical that destroying the biome by excising the prepuce would have a significant effect on the type and variety of flora present on the penis. By the same token, we could expect significant changes to female flora by excising the labia. If genital reduction surgery is deemed a beneficial prophylactic and is used to support a call for increased male infant circumcision, then we must also promote female infant labiaectomy for the same health reasons.

Avatar of: pfm


Posts: 1

May 31, 2014

Genital mutilation is common in many religions. It has often been taught in those religions that their ancient knowledge supercedes the science of today.

As recent as the 1950s, clitoridectomy for instance was practiced in Western Europe and the United States to treat 'ailments' in women as diverse as hysteria, epilepsy, mental disorders, masturbation, nymphomania, melancholia and lesbianism.


There are some who believe that slicing off the foreskin of a males penis will somehow magically keep them from being harmed by certain diseases. In every program that is promoting genital mutilation they also state that condoms and teaching them about sex is important. Actually the latter are the only aspects that can possibly stop HIV, cancer, or the other diseases often mentioned. Removing a piece of skin from the penis will *NOT stop the Aids virus.
The major Medical Associations of the world speak against it because there is no medical reason for it since the health risks outweigh the purported undocumented benefits.


Any time we have actions that give people a sense of being invulnerable when they are still very vulnerable we tend to promote confirmation bias and actually increase the diseases the placebo was intended to help decrease.


In fact, the foreskin's anatomical structure actually DECREASES the risks:


"Campaigns for mass circumcision in Africa began in 2007, shortly after three studies – in Kenya, South Africa, and Uganda – concluded that circumcision cut men’s risk to get HIV by 51% to 60% by reducing men’s risk to get HIV from sexual partners.
Those conclusions are based on assumption, not evidence. According to what men reported about sexual behavior in two trials, only a minority of their infections came from sex. It is, of course, possible that men lied about their sexual behavior. But with that argument, realize what has happened: The $1.5 billion enterprise to circumcise 20 million men in Africa is no longer based on evidence. It’s based on assuming away evidence. It’s based on a prior belief – inconsistent with evidence from these trials – that almost all HIV infections in African adults come from sex."

Avatar of: musa631


Posts: 1

June 3, 2014

I am here to learn from people who know more than I do. Naturally I am interested ointment all the sciences, although I know only a few in them
Avatar of: ml66uk


Posts: 2

June 3, 2014

This looks like more attempted justification of male circumcision.  We wouldn't cut off parts of ears or noses to reduce bacteria there, and if there were a study showing changes in the vulval microbiome from female genital cutting, it wouldn't justify cutting parts off girls.

Around 90% of the cells in or on a human body are microbes anyway, and many of these are essential to health.  Antibiotics sometimes cause problems by killing some of the beneficial bacteria, and fecal transplants actually introduce bacteria to improve health.

Several studies show lower rates of STI's in intact men than circumcised men btw.

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