Bacteria, Circumcision and HIV. Oh my!

Basically every place on our bodies is loaded with bacteria. All of these communities are important (I’ve written about some of the ways before) and more and more research seems to be finding that our microbes play an active role in fighting (or causing) disease.

So maybe it’s obvious that microbes in our swimsuit areas could be involved in sexually transmitted disease. OK, maybe not “obvious” but it may be the case with HIV and the penis microbiota. Did you know that circumcision reduces the rate of HIV transmission to men by 50 – 60%? That’s a pretty significant reduction (no pun intended). There are two major (and non-mutually exclusive) hypotheses as to how circumcision accomplishes this – morphological and bacterial. [SIDENOTE: if you are unfamiliar with the technical aspects of circumcision, I suggest Wikipedia – which has a lot of information but contains an image or two that may not be safe for work – or this Mayo Clinic site.]   

A 2-D representation of the uncircumcised groups' microbial communities at the start of the experiment (blue) and after 1 year (orange). Notice that blue and orange largely overlap.

Figure 1. A 2-D representation of the uncircumcised groups’ microbial communities at the start of the experiment (blue) and after 1 year (orange). Notice that blue and orange largely overlap.

The two-fold morphological argument is that the prepuce is especially full of HIV-susceptible cells and the uncircumcised sub-preputial environment is more hospitable to HIV (which can’t live outside the human body for very long) which could give the virus a little extra time to find a susceptible host cell. Removal of the foreskin eliminates both of the morphological possibilities. But wait – there’s more! It also affects the microbes.

The bacterial hypothesis states that circumcision alters the bacteria on the penis which reduces HIV-susceptibility. Previous research has shown that certain bacteria can elicit inflammation via an immune response that basically recruits HIV-susceptible cells. So – if circumcision alters the microbiota in such a way that HIV-susceptible-cell-recruiting bacteria are reduced, it may be the microbiota that is responsible for the medical benefits of circumcision.

Reporting in the open-access journal, mBio, Liu et al. (2013) attempt to elucidate the microbial dynamics of circumcision with a very simple experimental design. They begin by sampling the penile microbiota of 156 uncircumcised men. Approximately half of the men are then circumcised and all subjects are resampled after one year (presumably enough time that behavior is unaffected by the procedure).  All samples are analyzed using high-throughput sequencing of a universal bacterial marker and then the communities are from each man from the two time points are compared.  Several significant changes occurred to the microbial communities of circumcised men.

1. While all samples had similar bacterial communities at the start of the experiment, the uncircumcised mens’ microbial communities didn’t change much during the year (Figure 1), whereas the circumcised groups’ changed significantly (Figure 2).

2. All samples had similar numbers of microbial cells at the start of the experiment and both groups had a significant decrease in microbial cells at the end of the year. Uncircumcised men had a larger decrease.

Figure 2. Same as Figure 1 except this is for the circumcised groups' microbial communities. Notice that blue and orange are generally distinct. (Figures 1 and 2 taken directly from Liu et al. 2013.)

Figure 2. Same as Figure 1 except this is for the circumcised groups’ microbial communities. Notice that blue and orange are generally distinct. (Figures 1 and 2 taken directly from Liu et al. 2013.)

3. Many bacterial taxa changed in abundance. Notably, 15 bacterial taxa were significantly reduced in the circumcised group and 12 of these were strict anaerobes. This means that the circumcised environment selected for bacteria able to survive in an environment exposed to air.

4. The changes in bacterial taxa significantly changed the overall structure of the microbial communities.

It seems pretty convincing that circumcision affects the penile microbiota. Does this mean that these changes are responsible for the reduction in STI transmission? Maybe. Most of the circumcised group’s microbiota responded in similar ways (Figure 2) and that may coincide with the reduction of infections. Further study is needed but the authors contend that identifying a microbial “solution” might lead to lower transmission rates of HIV in areas where circumcision is less culturally acceptable.

Now, if you’re thinking “so did the uncircumcised men acquire HIV at a higher rate than the circumcised men?” the answer is no. All subjects remained HIV-negative throughout the study. In fact, they were chosen for that reason, since contracting HIV may have an effect on the bacterial communities of interest. (This study was performed on a subset of individuals participating in a much larger study that tracks HIV transmission – you can read more about transmission rates and behavior here.)

It’s pretty interesting to me how interrelated morphology, bacteria and disease can be. With all the recent studies showing links between microbes and health (obesity research comes to mind) and the accompanying medical advancements (did you read about the poop pills?!?!?), it’s an exciting time to be a microbial ecologist and a great time to be 9 months pregnant with a son (or is that just me?).

Liu, C., Hungate, B., Tobian, A., Serwadda, D., Ravel, J., Lester, R., Kigozi, G., Aziz, M., Galiwango, R. & Nalugoda, F. 2013. Male Circumcision Significantly Reduces Prevalence and Load of Genital Anaerobic Bacteria. mBio 4.

PS –Offered without comment, an observation about human sexual behavior:  According to Table 2,  all of the men in the study were married. Around 90% of the men in both groups had a single wife. Around 85% of the men said “no” to “Nonmarital sexual relationships” and around 58% of the men claimed to have one sexual partner throughout the course of the study.

24 comments on “Bacteria, Circumcision and HIV. Oh my!

  1. ml66uk says:

    The effect of male circumcision on HIV is far from clear.

    From a USAID report:
    “There appears no clear pattern of association between male circumcision and HIV prevalence—in 8 of 18 countries with data, HIV prevalence is lower among circumcised men, while in the remaining 10 countries it is higher.”

    Click to access CR22.pdf

    It seems highly unrealistic to expect that there will be no risk compensation. The South African National Communication Survey on HIV/AIDS, 2009 found that 15% of adults across age groups “believe that circumcised men do not need to use condoms”.

    It is unclear if circumcised men are more likely to infect women. The only ever randomized controlled trial into male-to-female transmission showed a 54% higher rate in the group where the men had been circumcised:

    ABC (Abstinence, Being faithful, and especially Condoms) is the way forward. Promoting genital surgery seems likely to cost African lives rather than save them.

    A recent article from Botswana
    “There is an upsurge of cases of people who got infected with HIV following circumcision.”

    Having genital surgery on a newborn baby boy to prevent HIV seems indefensible. It can’t possibly help unless he later in life has unsafe sex with an HIV+ partner, and it’s far from settled that it could help then.

    Would we even consider it for baby girls? There’s evidence that female circumcision could help against HIV:

    Stallings 2005
    ” A lowered risk of HIV infection among circumcised women was not attributable to confounding with another risk factor in these data.”

    Kanki et al. reported that, in Senegalese prostitutes, women who had undergone female circumcison had a significantly decreased risk of HIV-2 infection compared to those who had not. (Kanki P, M’Boup S, Marlink R, et al. “Prevalence and risk determinants of human immunodeficiency virus type 2 (HIV-2) and human immunodeficiency virus type 1 (HIV-1) in west African female prostitutes”. Am. J. Epidemiol. 136 (7): 895-907. PMID)

    • Hird says:

      thank you for this comment and especially for all the links! certainly behavior subsequent to the circumcision is going to have a huge impact – i hadn’t realized some people thought it would make them immune to HIV transmission. that seems like the major theme of the above links – that you still need to be using condoms. the lancet article i linked to above made it seem pretty clear that circumcision does, in fact, lower the chances of acquiring HIV, all else being equal, but i’m going to read some more about it.

      also, i didn’t mean to imply that i think all babies should be circumcised – especially for the sole reason of HIV prevention. the reading i’ve done about circumcision makes it sound like there are multiple health benefits – and the american academy of pediatrics (AAP) says “the benefits outweigh the risks”
      of course, that’s when the surgery is done properly and safely – in a hospital with qualified staff and appropriate/clean equipment.

      female “circumcision” is another ball of wax altogether, i think. it is – to my understanding and as it is generally practiced – not equivalent to safely-performed male circumcision. i will have to read more about the “benefits” of it – although from what i know, i doubt the AAP would say the benefits outweigh the costs!

      thanks again for the thoughtful comment. you’ve given me plenty to think and read about.

      • ml66uk says:

        It’s really easy to find circumcised doctors who are against circumcision, but surprisingly difficult to find male doctors in favor who weren’t circumcised themselves as children.

        The AAP position statement is here:

        It’s worth noting that it appears that none of the seven people on the task panel actually has a foreskin themselves, and at least two of them regard male circumcision as a religious obligation. One of them said he circumcised his son on his (the son’s) grandparents’ dining room table.

        I suppose it’s a good thing they didn’t look at operating on girls to prevent breast cancer. 11% of women get breast cancer, and 3% die of it, so the health benefits to the girls would massively outweigh the risks.

        The US position is very different to that of other national medical organizations:

        Canadian Paediatric Society
        “Recommendation: Circumcision of newborns should not be routinely performed.”
        “Circumcision is a ‘non-therapeutic’ procedure, which means it is not medically necessary.”
        “After reviewing the scientific evidence for and against circumcision, the CPS does not recommend routine circumcision for newborn boys. Many paediatricians no longer perform circumcisions.”

        Royal Australasian College of Physicians
        “After reviewing the currently available evidence, the RACP believes that the frequency of diseases modifiable by circumcision, the level of protection offered by circumcision and the complication rates of circumcision do not warrant routine infant circumcision in Australia and New Zealand.”
        (almost all the men responsible for this statement will be circumcised themselves, as the male circumcision rate in Australia in 1950 was about 90%. “Routine” circumcision is now *banned* in most public hospitals in Australia, and the rate is down to 12.4%.)

        British Medical Association

        Click to access Circumcision.pdf

        “to circumcise for therapeutic reasons where medical research has shown other techniques to be at least as effective and less invasive would be unethical and inappropriate.”

        The Royal Dutch Medical Association
        “The official viewpoint of KNMG and other related medical/scientific organisations is that non-therapeutic circumcision of male minors is a violation of children’s rights to autonomy and physical integrity. Contrary to popular belief, circumcision can cause complications – bleeding, infection, urethral stricture and panic attacks are particularly common. KNMG is therefore urging a strong policy of deterrence. KNMG is calling upon doctors to actively and insistently inform parents who are considering the procedure of the absence of medical benefits and the danger of complications.”

        This was written in direct reponse to the AAP’s statement:
        “The other claimed health benefits, including protection against HIV/AIDS, genital herpes, genital warts, and penile cancer, are questionable, weak, and likely to have little public health relevance in a Western context, and they do not represent compelling reasons for surgery before boys are old enough to decide for themselves.”
        (signed by 38 senior physicians, about half of them presidents or chairs of national paediatric or urological organisations).

        Female “circumcision” encompasses a range of procedures from the truly horrific to things far less invasive than the usual form of male circumcision.

        This link shows one form that’s fairly common in several countries, but banned in the USA:

        The AAP is the same organization that changed its policy on female cutting in 2010 btw saying “It might be more effective if federal and state laws enabled pediatricians to reach out to families by offering a ritual [clitoral] nick as a possible compromise to avoid greater harm.”
        They were forced to retract this about six weeks later.
        Dr Diekema, the chair of the committee said “We’re talking about something far less extensive than the removal of foreskin in a male”.

      • ml66uk says:

        More opposition to circumcision of children:
        “[30 September 2013] – At a meeting today in Oslo, the children’s ombudspersons from the five Nordic countries (Sweden, Norway, Finland, Denmark, and Iceland), and the children’s spokesperson from Greenland, in addition to representatives of associations of Nordic paediatricians and pediatric surgeons, have agreed to work with their respective national governments to achieve a ban on non-therapeutic circumcision of underage boys.”

        German Pediatric Association
        (very long, but very much against circumcision, and includes the following)
        “Therefore it is not understandable that circumcision of boys should be allowed but that of girls prohibited worldwide. Male circumcision is basically comparable with FGM types Ia and Ib that the Schafi Islamic school of law supports”

  2. George Hill says:

    It is hard to understand the intent of this document. Is the author considering the circumcision of a son who will soon be born?

    If so, there are far more important matters to be considered than the alleged effect of circumcision on HIV infection.

    1. The high complication rate of circumcision, the possible loss of the penis, and the possibility of death from infection or bleeding.

    2. the lifelong adverse effect on sexual function and pleasure.

    3. the lifelong adverse effect on emotional well-being caused by the loss of the erogenous part of the penis.

    4. the immoral and unethical nature of amputating a body part from another human being.

    • Hird says:

      i’m sorry you thought my intention was unclear – the post was meant to share the results of a study that found the microbial community on the penises of uncircumcised men are altered by circumcision. that finding is of interest because of previous research that indicates there may be a link between microbes, surgery and disease transmission. (and although i’ve been thinking about this topic because i’m pregnant, this post has nothing to do with that and i’m not going to get into a moral or personal discussion about my opinions on the matter…that’s a different topic altogether!)

  3. Camellia May says:

    Faulty reasoning. Non-circumcising Europe and Japan has far lower rates of all STI including HIV than the circumcising USA. There’s just as much logic showing circumcision increases rates of STI including HIV. People should be asking why HIV and other STI are so prevalent in the USA despite the high cost of medical spending and rate among developed nations?

    • Hird says:

      yes! we SHOULD be asking that question! i suspect sex education and safe sex practices play the largest role in all sorts of disease statistics – i don’t have any citations to back that up at the moment but i bet they’re out there!

  4. George Hill says:

    The cited paper was published in an open access journal. Such journals will print almost anything the authors pay to have printed, regardless of scientific merit.

    The list of authors include three who are paid professional promoters of circumcision who spend their time writing pro-circumcision articles. They are on the staff of the Bloomberg School of Public Health and are probably being supported by Michael Bloomberg who endowed the school. The names of the authors are Aaron Tobian, Maria Wawer, and Ronald Gray.

    Given the place of publication and the presence of three professional promoters of circumcision from the Bloomberg School of Public Health, there is no reason to believe the contents of the paper.

    • Amy Dapper says:

      While it is an unfortunate truth that a large number of predatory journals use the open access format to make money by publishing poorly (if it all) reviewed science, it is not the case that ‘open access’ is synonymous with bunk science. A number of rigorous scientific journals use the open access format to make research more accessible to the general public. The journal mBio falls in to this second category. It is not a predatory journal and the papers published there are reviewed carefully by experts in the field.

    • Hird says:

      Oh! I strongly, strongly disagree with your statements about open-access journals! In my opinion, open-access is a giant step forward for sharing publicly funded science with everyone. Certainly some journals are predatory and are strictly for-profit and will publish anything (I’ve written about this topic as well: and But mBio is an affiliate of the ASM and their publishing policies (including peer-review) give me no reservations about believing the findings. Accusing them of falsifying science to push their personal agendas is pretty serious.
      Also, it does seem that at least some of the authors are “pro-infant circumcision” but this could be based in their experiences and research. I doubt anyone is paying them to promote circumcision (who would benefit from that?) and I especially doubt Michael Bloomberg has anything to do with any of this.
      But back to the most important part: Science needs to be transparent and repeatable, which is why open-access articles are so important. Authors need to investigate the journals they publish in and be wary of many journals out there, but mBio doesn’t seem to be one of them (in my opinion).

  5. Ron Low says:

    Even IF the postulated model explained the results of the three large African RCTs on female to male transmission, nothing has yet explained the OPPOSITE male-to-female transmission effect. In the only RCT on circumcision and male-to-female transmission Wawer/Gray reported in 2009 that cutting HIV+ Ugandan men made them 50% MORE likely to infect their partners with deadly HIV.

    THIS might explain why the mostly-cut US has three times the HIV incidence seen in Europe where circumcision is rare.

    And the supposed protective effect for males is also highly questionable. Most of the US men who have died of AIDS were circumcised at birth.

  6. Chris Smith says:

    Whether not circumcision is ethical, moral, or safe, has absolutely zero bearing on whether or not there are changes in microbial communities following circumcision, which is what this article is about.

    Likewise arguments from authority… The accomplishments and educational achievements of those advocating or opposing circumcision tells us little about the strength of data supporting their claims. (For that matter, the business models of the publishers, or the source of endowment funds, tells us nothing about the rigor of a study).

    Circumcision either does, or does not, cause changes in microbial communities. Circumcision either does, or does not, change rates of HIV transmission. These are empirical questions to be addressed through data, not moral questions to be settled by appeal to one’s preferred wise oracle, or by issuing ad hominem attacks against those with whom one disagrees.

    • ml66uk says:

      I think it’s clear there will be changes in microbial communities following male circumcision, just as there will be following female genital cutting, or removal of any other parts of the body. It was stated as a fact though that “”circumcision reduces the rate of HIV transmission to men by 50 – 60%” when the evidence for this is highly contentious. It’s also suggested that the changes in penile microbiome mght account for the disputed changes in HIV transmission, and this seems even harder to defend.

      Regrettably, science isn’t as empirical as it perhaps should be, and researcher bias is a real problem. It wasn’t too difficult for the tobacco companies to find researchers who found that a link between cigarettes and lung cancer couldn’t be proven for example, and the extent of the risk of passive smoking is still very contentious. Similarly, the results of research on the existence, causes, extent, and cost of climate change.seem to depend on who’s funding the research. The position on male circumcision of the AAP seems to be almost the opposite of the positions of most other national medical organizations, yet they’re all looking at the same studies and data.

      • Hird says:

        Maybe it does seem obvious that the microbial communities will change with morphological modification – but knowing how it changes is not. The researchers found a significant shift in specific taxa of anaerobic bacteria – IF bacteria are responsible for a decrease in HIV transmission, this information might lead to a prophylactic or something that would prevent anatomical modification. But we won’t know until we study it.
        Also, I’m not sure how different the AAP’s opinion is from many other medical organizations – they say specifically they do NOT recommend universal circumcision of newborn boys. I think the statement “Evaluation of current evidence indicates that the health benefits of newborn male circumcision outweigh the risks and that the procedure’s benefits justify access to this procedure for families who choose it.” ( is just meant to ensure that people who choose it don’t have excessive restrictions or barriers to getting it done.
        You’re definitely right about the tobacco industry and climate change research, though. Human bias can influence science in negative ways for sure…

    • Ron Low says:

      Again the HIV studies are widely refuted,

      But EVEN IF this present study’s observed changes in fauna type and number were somehow responsible for reduced HIV susceptibility there is ZERO evidence that circumcision is best way to effect the change in fauna.

      Men could for example wear their skin rolled back off the glans to let the glans and foreskin dry. This FREE simple painless bloodless reversible experiment was not tried by the Kisumu, Rakai, or Orange Farm HIV researchers because they didn’t go to Africa to help Africans. They went there to justify circumcision.

      Nothing they did and nothing in this present research has any bearing whatsoever on a child’s right to be left intact to eventually make his own rational assessment of the evidence at responsible age.

      • Chris Smith says:

        Yep, Ron. You’re right. None of this has any bearing on a child’s right to be left intact. That is exactly my point. People are using this empirical result as an opportunity to get on a soap box and preach their own views about something that is only tangentially related.

        Nothing that Hird wrote is advocating forced circumcision. Indeed, Liu et al suggest that manipulating the microbial biota may be an alternative to circumcision. Why the suggestion that it may not be circumcision per say that shapes the risk of HIV transmission has engendered such a flame-fest from the anti-snipping community is a bit hard to fathom.

  7. Hi Hird, you might be interested to read about information regarding the function and purpose of the foreskin.

    First, this is an excellent educational video about circumcision narrated by Dean Edell, MD:

    Second, a 2007 study by Sorrells, et al., tested the fine touch sensitivity of a group of circumcised men and a group of intact (uncircumcised) men using the Semmes-Weinstein monofilament touch-test. The study found that the foreskin has dense concentrations of nerve endings called Meissner’s corpuscles and contains nearly all of the fine-touch nerve endings found in the penis. This type of nerve ending is found in the other erogenous zones and provides erogenous pleasure during sexual activity. Sadly, circumcision removes most if not all of those nerves.

    Click to access sorrells_2007.pdf

    Using data from that study, these color-coded diagrams show the areas of penile sensitivity. As you can see, the most sensitive parts of the penis are removed by circumcision:

    Third, the foreskin acts as a linear bearing during intercourse, making the experience more comfortable and pleasurable for women. This site explains how this works:

    Many women in America experience vaginal dryness, discomfort, or even pain during intercourse. Unfortunately, many people assume that this is due to a problem with female anatomy, but it is much more likely the fault of the modifications made to their partner’s bodies.

    Before I learned about the functions of the foreskin, I was in favor of circumcision, but now, I know that it’s not something I would ever force on a child who cannot consent.

  8. I dont understand the people who are against circumcision. It is like the anti-muslim/ anti-semitic discussion all over again. I dont deny that there might be male grown ups who didnt want to have a circumcision due to what ever reason. But that is far from the majority! Those people are the exeptions and might have a traumatic experience because of the lack of expertise and knowledge of the medical doctor.

    In the Netherlands for example, the urologist’s first years residents are performing a circumcision in the hospital. Beacause it is a relative easy surgical intervention. However these medical doctors who are being trained and educated to become a urologist do not have any experience at all. They might perform these interventions lets say 5-10 times a year. So therefor, there are several circumcision clinics such as: who are treating over 1000 boys per year per MD. That is called experience. And complications reduce to almost zero.

    So if we change the question and if we care about the health of these childeren, the question should be: How can circumcisions take place with a minimum af complications. The cons are then reduced and the pro’s increased. To be straight forward: without complications: circumcisions will not affect the health in any way. Not physically and not mentally. If there is a small chance that it could reduce the risc of HIV, the more reason circumcisions need to be promoted.

    • tlctugger says:

      Circumcision removes valuable sexual parts. It is not for any person to decide what ANOTHER PERSON’S sexual experience will be like.

      Infant circumcision is very haphazard absolutely without regard to the experience level of the cutter. There’s no right way to do a wrong thing. Many of the worst unintended effects happen during healing, notr during the cutting. And every circumcision takes away valuable sexual parts. Don’t value those parts? Fine. Cut your OWN parts off.

      Protecting the rights of ALL children without regard to gender, age, or creed is the opposite of religious discriination.

      • Since when does foreskin play any rol as a sexual part? This is new to me… And please do not say that it has its role because it covers the glans. because in erection that is not always true. You can use a condom or anything else if a man is afraid that he might ejaculate earlier. Without foreskin, it takes training… And training is good… And yes, i have had a circumcision too. And i am very glad my parrents arranged it, before i even can remember anything.

        If you a havent had a circumcision, then you know that there will always be the production of smegma between the foreskin and the glans, wich is discusting. a circumcision has nothing to do with mutilation. I noted that those few men, who do have a problem with their circumcision are not the majority. And I am not talking about 40% – 60%, but more about 1,5 % – 98,5%!!

      • ml66uk says:

        The inner foreskin is packed with nerve endings. It’s not just there to protect the glans, and like you say, in many men (including me), it fully retracts when erect anyway. The glans isn’t especially sensitive anyway. Even on a circumcised man, it’s not the most sensitive or pleasurable part – it’s normally the scar line, or the frenulum if that wasn’t removed. Skeptical? Try reaching an orgasm stimulating only the glans and the shaft an inch or more below the sulcus (the rim). You’ll probably find that the bit in between is far more important than you thought, and that’s what’s left of your foreskin.

        It’s worth remembering that no-one except for Jewish people and Muslims would even be having this discussion if it weren’t for the fact that 19th century doctors thought that :
        a) masturbation caused various physical and mental problems (including epilepsy, convulsions, paralysis, tuberculosis etc), and
        b) circumcision stopped masturbation.

        Both of those sound ridiculous today I know, but that’s how they thought back then, and that’s how non-religious circumcision got started. If you don’t believe me, then google this: “A Short History of Circumcision in North America In the Physicians’ Own Words”. Heck, they even passed laws against “self-pollution” as it was called.

        Women produce more smegma than men btw, but we don’t cut parts off baby girls to make it easier for them to keep clean. I’ve only ever actually seen smegma twice, when I’ve had to go days without a shower due to camping trips.

        Personally, I’d pay a year’s salary rather than be circumcised. Why would I want the most sensitive and pleasurable parts cut off?

      • Chakir Mousaoui, please see my post above for links describing how the foreskin is important for sex. I know it is suprising – I was circumcised as a baby, and I didn’t know about this either.

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