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Genetic Linkage

My Microbiome

I'm reposting this 2-year-old blog about the various bacterial outposts in the human body, in celebration of today's publication of the microbiome of a very special, intimate place. (I can say no more because it is embargoed until 2PM, when I will be traveling.)

Yesterday I committed a terrible crime. I walked away from a treadmill at the Y without scrubbing the handles.

“Ricki, get back here,” admonished the attendant as I headed for the elliptical. “You forgot to wipe down!”

“But I’m not sweating, and I never get sick. I won’t pass along Rocky mountain spotted fever or leprosy.”

“Sorry, it’s the rules. We don’t want to give anyone any nasty bugs, do we?”

“Actually, the immune system needs exposure to foreign antigens,” I said, launching into a spirited account of the roles of T and B cells in mounting an immune response.

“Just wipe down the machine,” muttered the attendant. So I went for the detergent and paper towels.

Apparently she had no clue that we are, all of us, walking bags of germs, ecosystems of an astounding diversity of microbial communities. In fact, 90% of our cells are not actually our own, but members of our microbiome.

We’ve known that the intestines are chock full of bacteria for many years, even before Jamie Lee Curtis started singing about Activia night and day. In 2007, the National Institutes of Health began the Human Microbiome Project Project to systematically describe the critters within us.

Microbiome researchers sample and sequence DNA tags from our surfaces, innards, and secretions, then check the information against genome sequence databases. This gets around the tricky problem that most microbes refuse to grow in our Petri dishes or tubes. The goal of microbiome research is to better understand how we get sick. And the potential of the approach seems limitless.

In July 2007 came what is still my favorite analysis of the human microbiome, the loaded diaper study. Researchers at Stanford University tracked the turds of 14 healthy babies, from their very first loaded diapers to the poops closest to their first birthdays. Although the baby bacteria were quite different at the outset, by the end of the year, their communities resembled those in the adult digestive tract.

Microbiome research is practical. Consider the
penis microbiome. Researchers in the US and Uganda probed the bacterial residents of the members of 12 HIV-negative Ugandan men pre- and post-circumcision. Several types of anaerobic bacteria (those that can live without oxygen) thrived in the uncircumcised organs, but couldn’t be found on the better-ventilated circumcised ones. And those bacteria are the ones that cause vaginal infections and trigger inflammation that eases HIV infection. The human vaginal microbiome is under scrutiny too, at Virginia Commonwealth University and the University of British Columbia.

Although most researchers still seem unusually enamored with probing gut bacteria, the mouth and skin are areas of great interest, too.

The human oral microbiome database hails from the Forsyth Institute in Boston, and includes 600 types of bacteria that affect our dental health and breath. Researchers in Germany and China are comparing oral microbiomes from 120 people from all over the world to uncover clues to ancient human migration patterns. Meanwhile, investigators at the National Human Genome Research Institute wax ecological over their efforts to describe the human skin microbiome, comparing a damp armpit versus a dry inner elbow to a tropical rain forest versus a savannah. They sampled 20 sites on 10 volunteers, ranging from the back of the head, to inside the nostril, to the bottom of a foot to an ass cheek and crack.

But as far as I can tell, all of these studies omit the parts that grab or drip onto an exercise machine.

Stay tuned. Today's announcement refers to one of the parts mentioned above. Guess which one!
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