The Human Biome
NIH Human Biome Project

Most bacteria are, like people, “either good or simply present.”

— The Belly Button Diversity Project

The Human Microbiome Project identified many of the microorganisms found in the human body revealing that, because we each have unique experiences in varied environments, we each have a unique microbiomic fingerprint. It is constantly changing its composition to maintain the balance that allows us to survive and thrive together.

The number and variety of microorganisms living on and within us is hard to grasp:

  • Our body consists of 10% human cells and 90% microbial cells
  • Altogether they account for about 3% of our body weight, about 2 to 5 pounds
  • Of all the genes contained in the cells of our bodies, 99% are from our microbes; only 1% are human!

The Belly Button Microbiome

We’re going to work our way down to the genitals from the belly button – it’s just too interesting to skip. In 2011, a group of undergrads from North Carolina State University had the genius idea of enticing public interest in science by swabbing belly buttons for bacteria. They had no difficulty finding 60 volunteers among visitors attending a conference at the North Carolina Museum of Natural Science. The results astounded them.

The officially named ‘Belly Button Diversity Project’ found that most belly buttons harbored about 67 species of bacteria, with a range from 29 to 107. Overall, they identified over 2300 different species, of which over 1400 may be new to science. One navel housed a microbe that had previously only been found in the soil in Japan. He had never been in Japan. Another navel gave up two bacteria that are usually found in extreme locations: ice caps near the poles and thermal vents in the deep ocean. (These were found in a volunteer who volunteered that he had not bathed in several years.) While the majority of species identified were common skin microbes, none of the microbes were found in all of the navels and 30% of the navels did not contain the most common microbes. The chief researcher likened the belly button microbiome to a rainforest – diverse, beautiful, and containing secrets yet to be discovered.

The Human Microbiome

The human microbiome is a characteristic (unique to you) community of microbes interacting with each other and its host (you), in a dynamic interplay that is necessary for the functioning and health of the community and the host. More than ten thousand different types of microorganisms colonize our bodies – bacteria, fungi, viruses, and protozoa.

We have microbial ecosystems everywhere – in our gut, nose, mouth, throat, ear, urethra, penis, vagina, on our skin, in our breastmilk, everywhere. Some spots are more profusely jungled than others. Since microbes prefer dark and moist to clean and dry, the gatherings are sparser on the shoulder than they are in the armpit, for example.

The great majority of these microbial creatures are friendly, living right along with us, even streamlining necessary body functions that we’d rather not think about. Food digestion and fecal formation come to mind. There are the few miscreants (the pathogens) that give the rest a bad reputation. But pathogenic organisms make up only a tiny fraction of our microbiomes and these are normally held in balance by the other microbes. Illness may arise from ‘dysbiosis’ – a change from our usual biome diversity and composition that can impact our immune system and permit internal or external pathogens to prevail.

The Penile Microbiome

Yes, the penis has a biome, just like every other part of our bodies including the lungs, the placenta, and the urethra – all of which, at one time, were thought to be sterile. Each biological man has their own unique mix of bacteria inhabiting their genitals.

The normal microbiota of the biologically male genitals are found primarily within the distal urethra and on the skin. There are many fewer microbes on the penis than there are in the mouth or in the vagina, because most penile skin is external. The mouth and vagina are dark and moist environments covered in delicate skin (mucous membrane) – much more appealing to microbes.   

The uncircumcised penis has more of these characteristics and therefore harbors more anaerobic bacteria than a circumcised penis. Anaerobic bacteria, the kind that can cause the most difficult problems like pelvic inflammatory disease (PID), bacterial vaginosis (BV), and septic abortion don’t like sunlight and oxygen. Removing the foreskin exposes more penile skin to the air forcing the anaerobic bacteria to find someplace else to live. Overall, the lower bacterial load and fewer of the “bad” pathogens can result in a decreased risk of contracting HIV (human immunodeficiency virus), HPV (human papilloma virus) and HSV (herpes simplex virus), among other sexually transmitted infections (STIs).

In areas where the risk of acquiring HIV is high, some biological men are choosing to be circumcised. However, circumcision is a highly culturized tradition – globally about 30 to 40 percent of men are circumcised – so the decision is highly personal and is only one of many effective methods of STI prevention.

Besides what resides on the penis, microbes can also inhabit the biological male ureter, bladder, prostate, and ejaculate. According to Larry Forney from the University of Idaho, there are about 10 million bacteria in one milliliter (about 15 drops) of ejaculate. That’s compared to 100 million bacteria per milliliter of vaginal secretions. Vaginas make better petri dishes.

 Studies of the bacteria in semen identified three main varieties – one dominated by Prevotella (sounds like an Italian cheese), one dominated by Lactobacillus which is also the predominant bacteria in the vagina, and one with no dominant bacteria (polymicrobial). Effects of the differing biotas on the strength, motility, and number of sperm is under study – any one type is not yet known to be more correlated with male infertility than any other type. These dominant varieties seem to exist regardless of race or geographic location, however, may be influenced by age and hygiene.

The Vaginal Microbiomes

The vagina presents an opportunity to understand the collaboration of individual members of the microbiome with the host to maintain the health of both. The predominant species of bacteria in most vaginas is Lactobacillus. It’s the same bacteria that turns milk into yogurt and sourdough starter into bread. Yum! Estrogens produced by the hormones in the body are the source of the sugars that the Lactobacilli ferment to produce lactic acid. Hormonal birth control methods contribute estrogens too.

In the vagina, the lactic acid lowers the pH of the vagina to about 4 to 4.5, lower than the neutral 7 found in most of the rest of the body. This acidic environment is inhospitable to many pathogens and fungi, thereby preventing infections. When the numbers of Lactobacilli are low, like after taking antibiotics, an overgrowth of opportunistic bacteria can occur. For example, Candida, normally held in check by the low pH, can now overgrow into a full-blown yeast infection.

More than 50 microbial species have been found in the vaginal. The key is keeping them all in a healthy balance. Medications, douching, low estrogen levels, and the introduction of external pathogens can mess up the delicate balance. An unbalanced microbiome, called vaginal dysbiosis, increases one’s risk for acquiring HIV and other STIs, pelvic inflammatory disease (PID) and adverse pregnancy outcomes such as preterm birth and maternal and neonatal infections. We need to take good care of our microbiomes.

Our Microbiomes Together

Penises and vaginas have individual microbial characteristics – what happens when they interact? Mouths, penises, vaginas, and anuses get together and share their microbiomes. They adapt to each other, each contributing bacteria to the other. Aww, sweet! Like moving in together and mixing the silverware.

But vagina owners beware, says Dr. Janneke van de Wijert at the University of Liverpool, UK. Having a new sex partner “is a microbial assault on the vagina,” she says. “The vagina will mount an immune response against the bacteria, causing inflammation” – and that raises the risk of getting an STI.

During heterosexual intercourse, even though biological women have more microbes in their vaginal secretions, they are more vulnerable to acquiring STIs than biological men. Vaginal skin is fragile and the volume of semen left in the vagina exceeds the volume of vaginal secretions that are left on the tougher skin of the penis. More vaginas get STIs from infected penises, than penises get STIs from infected vaginas. Dr. Hunter Handsfield at the University of Washington Center for AIDS and STDs calls this “biological sexism.”

During anal sex, both women and men who have receptive anal intercourse are at higher risk of acquiring STIs. The lining of the rectum is composed of the more porous and fragile mucous membrane too. And the rectum is home to microbes from the gastrointestinal (GI) tract that weren’t really meant for the genitals.

The Care and Feeding of our Genital Microbiomes

The exciting news is that the human microbiome is emerging as a potential target for personalized medicine. Treatments for diseases based on individual microbial signatures are being explored. These may include dietary adjustments, probiotics, synbiotics (synthetic microorganisms), and microbiome transfers (think fecal transplants).

To avoid infections that may need these new therapies, here are some recommendations on how to keep your microbiome healthy:

  • Use condoms – for vaginal and anal sex especially if you are not in a long-term monogamous relationship.
  • Biological women: Don’t douche! It messes with the balance of your organisms.
  • Don’t use chemicals, perfumes or other products on your genitals.
  • If you have abnormal secretions, smells, pain with or without sexual activity – get STI tested as soon as possible.
  • If you have a new sex partner, both of you get tested. Repeat in 3 months if either of you had other recent partners.
  • Eat right. Don’t feed the yeast with sugar.
  • Cotton underwear during the day, no underwear at night. Give your genitals some air!
  • Practice good hygiene so you don’t come home with a microbe from Japan or from deep in the sea!

Watch for news on the human microbiome. We still have much to discover. I think we’ll have some important breakthroughs in the near future.

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One Comment

  1. Sad for the elderly who have to wear incontinence clothing. You can’t “air out” your genitals, because you’d need a plastic bath to sleep in. It’s just part of aging, and more proof that the genetic process of aging is designed to kill you before you get old, to make room for the next generation. Personally, I never had kids, and won’t, so the next generation can go…..

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