Some disease sufferers have benefitted from fecal transplantation, in which a healthy person’s stool is transferred to a sick person’s colon. Illustration by Oliver Munday

One morning last fall, Jon Ritter, an architectural historian living in Greenwich Village, woke to find an e-mail from a neighbor, who had an unusual request. “Hi Jon, This is Tom Gravel, from Apt. 4N,” the e-mail began. “I wanted to check in and see if you may be open to helping me with a health condition.” Gravel, a project manager for a land-conservation group, explained that he had Crohn’s disease, an autoimmune disorder that causes inflammation of the intestinal tract along with unpredictable, often incapacitating episodes of abdominal pain and bloody diarrhea. His doctor had prescribed a succession of increasingly powerful drugs, none of which had helped. But recently Gravel had experimented with a novel therapy that, though distasteful to contemplate, seemed to relieve his symptoms: fecal transplantation, in which stool from a healthy person is transferred to the colon of someone who is sick. He hoped to enlist Ritter as a stool donor.

“I realize this is really out there,” Gravel wrote. “But I think you and your family are the nicest people in our building, and I thought I might start with lucky you.”

Crohn’s disease affects as many as seven hundred thousand Americans, but, like other autoimmune disorders, it remains poorly understood and is considered incurable. (Autoimmune disorders are thought to arise when the immune system attacks healthy tissue, mistaking it for a threat.) The standard treatments for Crohn’s often don’t work, or work only temporarily, and many have serious side effects. When the disease cannot be managed by drugs, surgery to remove part of the colon is often the only option. Gravel, who is thirty-nine, is slight and mild-mannered, with delicate features and floppy brown hair. He had endured nearly three years of debilitating symptoms, as well as a shifting regimen of enemas, suppositories, shots, supplements, and, for several months, intravenous infusions of Remicade, a potent immunosuppressant, at a cost of more than twelve thousand dollars each. “I would tell my wife in the morning, ‘I’m getting out my arsenal,’ ” Gravel told me.

Even so, blood tests continued to show high levels of inflammation. His daily life was governed by calculations of proximity to the nearest rest room. “I’d get nervous if I had to go to the bank,” he said. The checkout line at Whole Foods was an ordeal. By August, 2013, Gravel had stopped all his medications and was trying to manage his disease through a strict diet of broiled meat and fish and puréed vegetables. His mother showed him an article from the Times about a man who had been nearly bedridden by ulcerative colitis—a condition related to Crohn’s—and who had largely recovered after a month or so of fecal transplants. Gravel found a how-to book on Amazon and bought the recommended equipment: a blender, a rectal syringe, saline solution, surgical gloves, Tupperware containers. His wife agreed to be his donor. Doctors and patient-advocacy Web sites stress that donors should be screened for transmissible diseases, but Gravel and his wife decided to skip this step. “She’d been healthy as long as I’d known her,” he told me.

His doctor was unable to offer advice, saying that too little was known about fecal transplants. Nor could he legally provide the procedure. The Food and Drug Administration regards fecal transplantation as an experimental treatment, and doctors must apply to the agency for permission before offering it to Crohn’s patients. Just as Gravel began to research the procedure, his wife received a diagnosis of breast cancer. They began daily transplants anyway, and soon he was feeling much better. But his wife was scheduled to have surgery, followed by chemotherapy. Gravel needed another donor, someone nearby. “I immediately thought of Jon,” he said.

A strapping forty-eight-year-old partial to organic food, Ritter exuded good health. “At first I was kind of shocked,” he told me. “Pretty quickly I realized I didn’t really have a problem with it. What he wanted was something I wasn’t using—that was going to waste.”

No one knows how many people have undergone fecal transplants—the official term is fecal microbiota transplantation, or FMT—but the number is thought to be at least ten thousand and climbing rapidly. New research suggests that the microbes in our guts—and, consequently, in our stool—may play a role in conditions ranging from autoimmune disorders to allergies and obesity, and reports of recoveries by patients who, with or without the help of doctors, have received these bacteria-rich infusions have spurred demand for the procedure. A year and a half ago, a few dozen physicians in the United States offered FMT. Today, hundreds do, and OpenBiome, a nonprofit stool bank founded last year by graduate students at M.I.T., ships more than fifty specimens each week to hospitals in thirty-six states. The Cleveland Clinic named fecal transplantation one of the top ten medical innovations for 2014, and biotech companies are competing to put stool-based therapies through clinical trials and onto the market. In medicine, at any rate, human excrement has become a precious commodity.

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Science writers love to cite the freakish fact that for every one of our cells we are hosts to ten microbial ones, and nowhere are there as many as in our digestive tracts, which house about a hundred trillion bacteria, fungi, viruses, and other tiny creatures. (As one gastroenterologist put it to me, with only mild exaggeration, “We’re ten per cent human and ninety per cent poo.”) Collectively, this invisible population is known as the gut microbiome, and lately it has become an object of intense scientific interest. “You can hardly mention a disease today where something hasn’t been looked at regarding the microbiota,” Lawrence Brandt, a gastroenterologist at Montefiore Medical Center, in the Bronx, who was among the first physicians in this country to perform fecal transplants, told me.

For years, efforts to study the microbiome were stymied by the number of species involved and the difficulty of culturing finicky strains in the lab. But the advent of genetic-sequencing technology has made it possible to identify microbes by their DNA, spawning a frenzy of research, whose highlights, routinely catalogued in the popular press, can have an air of science fiction. (A recent headline in the Times: “how bacteria may control our behavior.”) Much of the research is still preliminary, and a lot of it depends on stool, which by dry weight is roughly forty per cent microbes and remains our best proxy for the brimming universe within.

FMT, the chief medical application of microbiome research to date, is also at a rudimentary stage. The procedure has been proven to work only in the case of a single disease: a bacterial infection known as Clostridium difficile. The infection, which causes symptoms similar to Crohn’s, afflicts more than five hundred thousand people each year, killing fifteen thousand of them, almost all hospital patients who received antibiotics. Like a weed killer that slays not just the invading vine but, inadvertently, the entire garden, broad-spectrum antibiotics, which are prescribed prophylactically to patients undergoing surgery, can destroy gut flora, making it easier for C. difficile to take hold. Moreover, the standard treatment for the disease—vancomycin, itself an antibiotic—is often ineffective against drug-resistant, “hypervirulent” new strains.