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6 Ways to Transplant Fecal Matter, at Home or at the Hospital

How doctors perform fecal transplants today. An extra to Bryn Nelson's feature-length look at the next big thing in health care.
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Micrograph of a colonic pseudomembrane in Clostridium difficile colitis. (Photo: Nephron/Wikimedia Commons)

Micrograph of a colonic pseudomembrane in Clostridium difficile colitis. (Photo: Nephron/Wikimedia Commons)

Fecal microbiota transplants, which involve getting donor poo into patients’ bodies, are being investigated for the treatment of a number of conditions, including inflammatory bowel disease and infection with the bacterium Clostridium difficile. Here are six ways that doctors perform the procedure.


Doctors insert poo through a patient’s nostril, down the throat, and into the stomach using a thin, flexible feeding tube. Embraced by some clinicians who want a simple delivery method that doesn’t require sedation or a colonoscope, the technique is vigorously opposed by others.

“The problem with it is, patients hate tubes stuck down their nose. I mean they hate it more than anything you could do with them,” says Colleen Kelly, a gastroenterologist with the Women’s Medicine Collaborative in Providence, Rhode Island. “I still worry that somebody’s going to throw up all that stool that you put down and it’s going to be a big mess.” Other providers worry about the risk of an already-ill patient aspirating feces into their lungs and getting pneumonia.

For all fecal transplants, doctors and advocates emphasize the critical importance of screening donors for any pathogens or medical conditions that could lead to complications for the recipient.

The nasogastric method “should be abolished,” says Thomas Borody, founder and director of the Centre for Digestive Diseases in Sydney, Australia. “Poo is not made to go down the small bowel and you get translocation of bacteria, they give you bactaeremia and fevers,” he says. “Can you imagine having a nasogastric infusion of someone’s poo and then you burp or you vomit?”

Even so, some pediatricians prefer the technique’s simplicity. In 2010, doctors at Harvard Medical School in Boston, Massachusetts, used the technique in the first published demonstration of a successful fecal transplant in a young child, a toddler with recurrent C. diff. David Suskind, a pediatric gastroenterologist at Seattle Children’s Hospital, specifically chose the technique for a clinical trial focusing on children with Crohn’s disease and ulcerative colitis. “Our microbiome is not limited to the colon,” he says. A nasogastric tube infusion, he believes, may also reseed the small intestine, which can be equally inflamed in Crohn’s disease.


Using a feeding tube, doctors insert poo through a patient’s nostril, down the throat, and past the stomach to the duodenum (the first section of the small intestine), thereby reducing the risk of regurgitation.

In a small but influential randomized controlled trial from the Netherlands, clinicians cured 81 percent of patients with recurrent C. diff. after one nasoduodenal infusion, and 94 percent after two infusions. In comparison, they cured only 31 percent of patients given vancomycin and only 23 percent of patients given vancomycin and a thorough flushing of the intestinal tract.

Max Nieuwdorp, a co-author of the study and associate professor of internal medicine and endocrinology at the Amsterdam Medical Centre, is among the doctors who prefer a nasoduodenal tube to a colonoscopy. The nasoduodenal method, he says, is more convenient in patients with diverticula, a common condition in older people in which small pouches pinch off from the colon’s main channel.


Tried on an ad hoc basis in the 1950s, the idea of encapsulating donor poo in a pill gained momentum after researchers at the University of Calgary in Canada presented the results of their clinical trial at the 2013 IDWeek Conference in San Francisco. In a proof-of-principle trial of 27 patients with recurrent C. diff., Thomas Louie and his colleagues gave each patient between 24 and 34 capsules. All subsequently recovered from their infections.

In Australia, Borody has developed his capsule-based technique, dubbed a “crapsule.” The technique could be a boon for patients who cannot tolerate a nasogastric tube or a colonoscopy, or who cannot retain enemas due to fecal incontinence. Taking his cue from the Canadian study, R David Shepard in Tampa, Florida, cured a nursing-home patient with C. diff. by giving her 35 capsules filled with poo from her daughter.

Transforming the highly bespoke process into a more widely available option, however, may require more rigorous randomized controlled trials and a method for mass production.


Doctors ease a colonoscope, a finger-wide hollow tube with an attached camera, up the colon of a sedated patient and then use a catheter-tipped syringe to inject a slurry of donor poo through the channel. Many gastroenterologists favor this method because they can reseed microbes in the upper colon and gather crucial information about its state.

“I think it’s important, especially when dealing with young patients who still have a lifetime ahead, to document what their colon looks like at the time of the procedure,” says Alexander Khoruts, a gastroenterologist and immunologist at the University of Minnesota in Minneapolis. “I’ve had a number of cases where I’ve done the colonoscopy and discovered they had Crohn’s disease that they didn’t know about.”

In a study of 77 patients with recurrent C. diff., representing cases from five U.S. medical centers, doctors cured the diarrhea with a colonoscopic fecal transplant in 91 percent of the cases. In 2012, doctors at the University of Chicago reported the first successful colonoscopic fecal microbiota transplant in a child, a 16-month-old boy who had contracted C. diff. six times. Within 24 hours of the transplant, the boy’s symptoms had completely disappeared.

Borody uses a two-infusion technique via colonoscopy. For irritable bowel syndrome with severe diarrhea, his success rate hovers around 85 or 90 percent, he says. For C. diff. infections, it’s nearly 100 percent. “This is an overnight difference,” he says. Some doctors, like Shepard, supplement a fecal colonoscopy with an endoscopy method that delivers poo via an endoscope down the throat to the jejunum, the midsection of the small intestine. Shepard hasn’t yet published his results, but for curing C. diff. infections, he says he hasn’t had a failure yet.


Using a sigmoidoscope, a hollow tube similar to a colonoscope but shorter, doctors insert donor poo into the lower portion of the colon only: the sigmoid. Colleen Kelly began performing fecal transplants via colonoscopy on sedated patients, then switched to sigmoidoscopy, a procedure she says is safer, cheaper, and more convenient because it doesn’t require sedation. The procedure, she says, has been just as effective, and still allows her to examine the lower portion of the colon. Kelly hasn’t fully published her results, but says that in more than 130 C. diff. patients she’s treated so far, she has achieved an overall cure rate of about 95 percent, mostly with just a single transplant.


Although far cheaper and less invasive than a colonoscopy, a fecal enema often must be repeated multiple times because the donor poo can’t be introduced high enough into the colon for the bacteria to effectively colonize the lining. Enemas are harder for patients to retain and can be messier than other methods.

For all fecal transplants, doctors and advocates emphasize the critical importance of screening donors for any pathogens or medical conditions that could lead to complications for the recipient.



Medicine's Dirty Secret: Fecal Transplants Are the Next Big Thing in Health Care

This post originally appeared on Mosaic as “6 Ways to Transplant Poo” and is republished here under a Creative Commons license.