Circumcision Alters the Penis Microbiome

Fact checked by Dr. Mohd Shafiz Mohd Zaini

Circumcision is a medical procedure that doctors perform on male human beings. It involves the surgical removal of the foreskin of the male genital part. A circumcised penis has permanently exposed glans. Once circumcision takes place, the glans tend to undergo keratinization. Circumcision can either be performed medically or traditionally. Traditional circumcision is mostly practiced in sub-Saharan Africa as an initiation rite of passage from childhood to adulthood for adolescents and young men.

Other than the change in the physical characteristics of the male genitalia, circumcision alters the penis microbiome. Wondering how that occurs? Let’s get right into it.

Does the Penis Have a Microbiome?


Yes, the penis has a microbiome. It comprises the wide assemblage of micro-organisms that inhabit it. The male penis provides surfaces with ideal environmental conditions like oxygen, moisture, temperature, and nutrients, fostering the growth, survival, and symbiosis of microbes and disease-causing pathogens such as bacteria, fungi, and viruses.

However, bacteria thrive the most. The environment around the penis provides ideal habitation sites for facultative, aerobic, and anaerobic bacteria. Some common bacterial species on a male penis include Lactobacillus spp, Staphylococcus spp, Streptococcus spp, and Corynebacterium spp.

Circumcision and the Penis Microbiome

Male circumcision changes a penis’ microbiome. The removal of the foreskin exposes the glans, which in turn completely alters the moisture content of the penis, the level of oxygen from an enclosure to a more open environment, and the temperature. It also reduces the surface for attachment and accumulation of microbes. That, in turn, affects the micro-organism abundance and diversity in the penis microbiome. There’ll be the reduction of anaerobic bacteria on the penal surface covered by the foreskin, while aerobic bacteria whose existence is favored by oxygen abundance can increase drastically (4). A different study on the difference of bacterial diversity and abundance on the penis of circumcised and uncircumcised men showed a 33.3% reduction in bacteria on the penis of the circumcised participants as compared to the uncircumcised. That was mostly attributed to the anaerobic bacterial colonization decrease of 12 species.

Studies have also shown a reduced rate of HIV infections between circumcised males and female sexual partners(8). Circumcised males generally have a lower risk of HIV than their uncircumcised counterparts(6). The anoxic environment of the subpreputial space may support pro-inflammatory anaerobes. That can activate Langerhan cells to present HIV to CD4 cells in draining lymph nodes on the penis skin surface. That may play an important role in protecting a circumcised individual from HIV and other sexually transmitted diseases. Reduced HIV risk can also be attributed to the reduction in local immune inflammation in the penile tissues, which generally prevent the loss of epithelial barrier integrity and facilitate the reduction in the density of penis cells susceptible to HIV.

How do Men Get Bacteria on Their Penis?

There are multiple ways men can get bacteria on their penis. It can be through oral, anal, or vaginal sexual activity with other male or female sexual partners.

Bacteria can also get to the penis through physical touch during urination. Other means include non-voluntary touch with fabric surfaces or water during a bath.

Are Circumcised Men More Hygienic?

Second-Circumcision-InvolveTechnically, circumcised men are more hygienic than uncircumcised ones. A penis with a foreskin provides an ideal environment for accumulating smegma (a mixture of dead skin cells and bodily oils), which can harbor bacteria and pathogens. If not cleaned regularly, the penis can exhibit awful smells.

A circumcised penis is more hygienic as it’s easy to clean and remains dry and free of the accumulation of smegma (7). Uncircumcised men predominantly tend to harbor pathogenic bacteria in the penis. A study conducted to assess the presence of pathogenic bacteria in circumcised and uncircumcised men observed opportunistic pathogens such as Staphylococcus aureus, Enterococcus sp, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella spp were more present on men who have not undergone the cut (5).

What Are The Positive Effects of Circumcision?

There are multiple benefits a man can get from circumcision (1). These include;

  • Reduced risk of contracting urinary tract infections
  • Reduced risk of contracting and transmitting Human papillomavirus and sexually transmitted diseases
  • Better hygiene
  • Prevention of phimosis (the inability to retract the foreskin)
  • Prevention of paraphimosis (the inability to return the foreskin to its original position)
  • Protection against penile cancer and lowers the risk of cervical cancer among female sexual partners
  • Prevention of balanitis and balanoposthitis (inflammation of the glans and inflammation of the glans and foreskin, respectively)
  • Prevention of physical injury such as the sticking of the foreskin in a zipper
  • Ease in wearing a condom on a circumcised penis

What Are The Negative Effects of Male Circumcision?

Circumcision has minimal negative effects on general health and anatomy. If the doctor performs it correctly, the procedure is harmless. However, the patient may experience pain and discomfort after the procedure and healing.

A study conducted in Kenya found that circumcision has no significant effect on sexual function or sexual satisfaction (3). Overall, circumcision has more known positive effects than negative ones.

Can Men With Foreskin Get BV?

No, men can’t get bacterial vaginosis (BV) due to the absence of a delicate balance of bacteria in the penis, as it’s with women with their vaginal microbiota. Additionally, bacterial vaginosis is not transmitted like other sexually transmitted diseases. However, female sexual partners of men who have not undergone circumcision have a higher likelihood of developing bacterial vaginosis. That’s because an uncircumcised penis can harbor and form an ideal habitat for bacteria, which may alter the lactobacilli and other vaginal microbiota balance resulting in bacterial vaginosis. The disbalance tends to result in the flourishing of harmful bacteria, which cause the infection (2).


Generally, circumcision is an important medical and cultural practice that has multiple health benefits to a male individual and their female sexual partners if embraced. If done early, when a boy is young towards adolescence, the glans’ keratinization is more effective. Moreover, healing can be quicker and less painful.


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