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Advances in genetic technology have opened a window into the populous and powerful world of microbial life in and around the human body. (Illustration by Stephanie Dalton Cowan)

Microbes: The Trillions of Creatures Governing Your Health


Scientists are just now beginning to recognize the importance of the vast community of microbes that dwells inside us


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In a procedure room at Rhode Island Hospital in Providence, a gastroenterologist named Colleen Kelly sprays a little air freshener, says “Breathe through your mouth” and then opens a plastic container of donor material, delivered fresh this morning by a relative of today’s patient. Kelly mixes it into a half liter of saline solution, then shakes it up like a bartender mixing a mai tai. She draws the liquid off into a half-dozen syringes the size of handheld bicycle pumps, and then it’s time to wheel in the patient.

The idea of fecal transplants is not new. Veterinarians have long used them to treat livestock with digestive troubles. Human cases in the United States, though rare, date back at least to the 1950s. But the procedure has become more common recently because it seems to cure C. diff. infection. Janet O’Leary, a medical imaging technologist in Massachusetts, went to Kelly for the procedure last October. “I told my boyfriend what I was going to do,” she recalls, “and he said, ‘I absolutely don’t believe it. You’re making this up.’”

Her personal physician felt almost as horrified. “It’s considered fringe, and this is how medicine in America works,” O’Leary says. “It’s not a drug. Nobody’s making money off it. Yet. It’s not being pushed by a dozen companies. It’s just a natural way to get the normal flora back in your gut. My response is that there is no ‘yuck factor’ for people who are this sick.”

O’Leary had come down with C. diff. after a vacation trip on which she used a powerful antibiotic for turista. Back home, her doctor prescribed another round of the same antibiotic, and the problem just got worse. A different antibiotic followed, and then repeated courses of a third antibiotic. It got so bad O’Leary couldn’t go to work at her hospital. She became a patient instead. “This wasn’t getting better. It was pretty scary, and the doctors were saying they might try another round of antibiotics, or I might lose part of my colon.”

Instead, O’Leary contacted Kelly, one of a few dozen gastroenterologists around the country now performing fecal transplants. The donor is usually a family member, says Kelly, and must be screened beforehand to ensure against introducing known pathogens. The procedure itself is a basic colonoscopy. But on the way back out, Kelly screws those bicycle-pump syringes into the instrument panel of her colonoscope and injects the contents at various points in the colon. The phrase is to “seed them through,” planting a healthy micro­biome like a landscaper installing a new garden.

Of 94 C. diff. patients she has treated, Kelly says, all but three have overcome the infection. She’s now participating in a National Institutes of Health study to test the effectiveness of the procedure against a placebo in a double-blind clinical trial. She also foresees a time when a carefully designed probiotic manufactured in a laboratory will obviate the need for a human donor. One researcher has already begun testing an experimental version. It’s named RePOOPulate.

For the rest of us, the idea of fecal transplants, or of ulcer-causing bacteria as our sometime-friends, or of babies being anointed into humanity at birth by their mother’s microbiome, will no doubt continue to sound a little gross for a while to come. But here’s a way to put that in perspective: Vaccination also sounded gross when Edward Jenner figured out in the 1790s that inoculating people with pus from a cow could protect them from smallpox. And it was gross in 1928 when Alexander Fleming began the process of turning a moldy growth into penicillin. But vaccines and antibiotics would go on, in time, to become the most important discoveries in the history of medicine, and they now routinely protect billions of people from disease.

Coming to understand our microbes not as enemies, but as intimate partners could change our lives at least as dramatically, with time and proper testing. Asked recently about the prospects for microbiome research, one scientist not directly involved put it this way: “To make an analogy, we’re roughly a year after Fleming found penicillin.”

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About Richard Conniff
Richard Conniff

Richard Conniff, a Smithsonian contributor since 1982, is the author of seven books about human and animal behavior.

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