Does Circumcision Change the Penile Microbiome? What Research Says About Flora, Infection Risk, and Infant Health

Circumcision changes the bacteria found under the foreskin. These changes may affect hygiene and health in infants. Learn how the penile microbiome differs before and after circumcision and what that means for infection risk and bacteria. Find out what recent knowledge says about how circumcision affects penile bacteria.

What Is the Penile Microbiome in Infants and How Does It Develop Before Circumcision

Did you know the skin around the penis, including the foreskin, is home to a unique mix of bacteria in infants? This is known as the penile microbiome—a collection of bacteria, fungi, and other microorganisms that naturally live on the penis. Before circumcision, the foreskin creates a moist, low-oxygen environment, which can encourage the growth of certain bacteria. These bacteria can include anaerobic bacteria under the foreskin, such as Prevotella and Porphyromonas, along with others like Staphylococcus aureus and E. coli.

While these bacteria are part of the normal skin flora, the bacterial flora under the foreskin can sometimes lead to inflammation or infections if the balance is disrupted. For example, the foreskin can trap moisture and secretions, creating a perfect space for certain microbes to thrive. This is why some parents choose circumcision for their infants—not just for cultural or religious reasons but also for the benefits of circumcision for infant hygiene.

Understanding how the penile microbiota composition develops in infants helps explain how circumcision may impact health. When the foreskin is present, it creates a unique environment. Removing it changes that environment completely, as we’ll see in the next section.

Scientific Studies on Microbiome Changes in Infant Boys After Circumcision

Circumcision significantly alters the penile microbiome. One major shift is the reduction in anaerobic bacteria under the foreskin. When the foreskin is removed, the moist, low-oxygen environment disappears, and the bacterial community changes. For instance, the Prevotella circumcision study found that Prevotella, a type of anaerobic bacteria commonly found under the foreskin, becomes much less common after circumcision. Other bacteria, like Staphylococcus and Corynebacterium, become more prominent.

These microbiome changes after circumcision can impact overall health. For example, fewer anaerobic bacteria may lower the risk of irritation or infections that could trigger inflammation. While the diversity of the penile microbiota composition decreases slightly after circumcision, the remaining bacteria tend to be those more typical of healthy skin.

This shift in microbial balance is a natural result of changing the environment of the penis. It shows how circumcision affects penile bacteria is not just about removing skin but also about reshaping the microbiome.

Why Reducing Anaerobic Bacteria in the Infant Penile Area May Lower Infection Risk

Let’s think about this: reducing certain bacteria = lowering the chance of infection. It’s a simple equation, and it explains part of why some parents choose circumcision. The anaerobic bacteria under the foreskin, like Prevotella and Porphyromonas, thrive in the low-oxygen space created by the foreskin. These bacteria can lead to local infections or contribute to higher risks of certain conditions later in life.

By removing the foreskin, the bacterial flora under the foreskin is reduced, and the environment becomes less favourable for anaerobic bacteria. This lowers the likelihood of inflammation, redness, or other problems. That’s one reason why many families consider the benefits of circumcision for infant hygiene.

While there are different opinions on circumcision, it’s clear that circumcision and infection risk are linked through changes in the microbiome. Fewer anaerobic bacteria = a lower chance of infections, especially those that can cause infant discomfort or health issues.

Can a Less Diverse Microbiome Be Beneficial for Infants After Circumcision?

Here’s an interesting question: does a less diverse microbiome mean a healthier one? When we talk about the penile microbiota composition after circumcision, the variety of bacteria decreases. However, in this case, less diversity may mean fewer pathogens.

For example, how circumcision affects penile bacteria shows that bacteria like Prevotella, Gardnerella, and Anaerococcus—which thrive under the foreskin—drop dramatically after circumcision. Instead, bacteria like Corynebacterium and Staphylococcus (which are part of normal skin flora) increase.

So, while the microbiome may become less complex, it becomes more stable and closer to what’s found on regular skin. This is why some parents see the benefits of circumcision for infant hygiene, as a simpler, less varied microbiome might reduce the chances of irritation and infection. It’s not always about having the most diverse microbial community—it’s about having the right balance for infant health.

How Infant Circumcision Affects UTIs, Local Inflammation, and Skin Flora Balance

Circumcision does more than just change the skin—it shifts the entire environment of the penis. Fewer anaerobic bacteria = lower risk of urinary tract infections (UTIs) in infants. Research has shown that UTIs are more common in uncircumcised boys, likely because the bacterial flora under the foreskin can sometimes travel into the urinary tract. By removing the foreskin, the chances of this happening are reduced.

Inflammation is another important aspect. The penile microbiome before circumcision can include bacteria that irritate the skin or cause infections. After circumcision, there are fewer such bacteria, which may mean less inflammation and discomfort for the infant. This is part of the broader connection between circumcision and infection risk.

In simple terms, changing the penile microbiota composition means changing the balance of skin flora, which can have practical benefits for infant health. Circumcision = fewer anaerobic bacteria = lower risk of infections and inflammation.

Dr. Mark A. Greenberg, B.Sc., MD, CCFP(AM), is a physician with over 20 years of experience performing infant circumcision and is dedicated to providing care with compassion and precision. His work at Dr. Greenberg’s clinic focuses on supporting parents in making informed decisions about their child’s health and well-being, including considerations around circumcision and public health microbiome impacts.

Which of these points surprised you the most? Let us know your thoughts—every family’s story is unique, and we’re happy to help with your questions!