Human waste has long been thought of as just that: everything the body doesn’t want or need. But new research is showing that feces may contain valuable organisms that can actually treat disease.

In a new paper published in JAMA, researchers led by Dr. Dina Kao, a gastroenterologist at the University of Alberta in Canada, and her colleagues report that fecal matter manufactured into a capsule was no worse than fecal matter transplanted by colonoscopy. Both procedures successfully reduced risk of repeated C. difficile infections by more than 90%. C. difficile (C. diff) infections can be caused by bacteria that are resistant to many antibiotics.

The advantages of a capsule over a colonoscopy, which is an invasive procedure that requires mild sedation, are clear. Any time people are sedated, there is a risk that their breathing will slow too much. Colonoscopy also comes with the risk of puncturing the intestinal wall, which can introduce infections that could be life threatening. The benefits of swallowing a capsule are also undeniable compared to swallowing — or trying to swallow — a feeding tube through which a slurry of fecal matter is flowing through. (That’s the way that doctors testing fecal transplants originally administered their doses.) That carries the risk of aspirating some of the fecal slurry into the lungs — not to mention the unpleasantness of introducing feces to the mouth area and accidentally breathing it in.

Fecal transplants are part of the burgeoning field of research involving the microbiome: the living universe of microbes, including bacteria, that live on and in the body. Unlike their disease-causing counterparts, these microbes work to improve human health. Certain bacteria, for example, are linked to lower rates of conditions like allergies, asthma, obesity and even some types of mental illnesses.

Studies have found that certain microbes in the digestive tract are linked to lower rates of C. difficile infection, which is mainly acquired in health care settings like hospitals and nursing homes. About 90% of people who receive fecal transplant by colonoscopy do not experience recurrent infections. Antibiotics can treat the infection, but anywhere from 10% to 30% of people will develop further infections, and each recurrence increases the risk of another one.

While certain microbiome populations can lower the risk of infection, it’s not clear whether the amount of bacteria in the gut is the key factor, or whether it’s the type of bacteria or even how the bacteria is delivered. In the study, Kao focused on understanding whether the way the gut bugs are delivered makes a difference. “The biggest question in this area has always been, what’s the best way to deliver the transplant?” she says. “I think with this study, we can see that maybe the capsule delivery format is the way to go if you are going to give this type of microbiome-based therapy.”

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All 116 people in the study had experienced at least three cases of C. difficile infection. They were randomly assigned to receive a fecal transplant by either capsules or a colonoscopy. The people taking the capsules had to swallow 40 of them in a single sitting, usually over 30 minutes to an hour. After 12 weeks, about 90% of people in each group remained free of additional infections.

That’s encouraging for patients who struggle with a poor quality of life while battling recurrent infections, which cause serious diarrhea several times a day along with severe cramping and dehydration. “Based on this study, I think it would be very reasonable to think about fecal transplant capsules as your preferred approach,” says Dr. Preeti Malani, professor of medicine at the University of Michigan, who wrote an editorial accompanying the study. “If it were myself or a family member, I think avoiding colonoscopy would be helpful.” She also notes that most people who have repeated infections are older, frail and in poor health, which makes an invasive procedure like colonoscopy riskier.

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But she also says that more studies are needed — first, to confirm the results that Kao found, and second, to better understand how the fecal transplant process works. One question is whether the bacteria are actually responsible for controlling the infection. A previous study found that a fecal sample that was sterilized to kill all the bacteria still resulted in fewer repeat infections, raising the question of whether there is something else in fecal matter that is beneficial. If bacteria are responsible, which bacteria are best, and how much are needed to treat the infection? These unanswered questions are why the Food and Drug Administration has not yet approved fecal transplants, but does allow doctors to apply for permission to perform them to treat people with C. difficile that does not respond to other therapies — as long as the patient is aware the transplant is still in the testing phases.

Kao is planning on studying the components of the fecal transplant to better understand what is helping to control the C. difficile.

In the meantime, while the idea of swallowing a capsule of poop may seem unpleasant, it may be the best way yet to control an otherwise devastating infection. When Kao asked the people in the study to rate their experience, more people taking the capsules than the colonoscopy said the process was “not at all unpleasant.”