By Mandy Oaklander
September 27, 2014
TIME Health
For more, visit TIME Health.

It’s an undeniably unusual donation from a healthy stranger—a sample of their digested waste that would otherwise be flushed down the toilet—but instead is infused, via enema, into a willing recipient suffering from a potentially life-threatening infection. The medical reason, to recolonize the disturbed gut bacteria introduced by the bacterial infection, is pretty logical, but this time, with healthy bugs. Still, the very idea of swapping feces may strike some as more gross than amazing.

That’s part of why they’re not a mainstream way of treating Clostridium difficile (C. difficile) infections, despite growing evidence that they can be effective. In the U.S., the Food and Drug Administration (FDA) has struggled with how to regulate the controversial therapy, deterring a lot of doctors from doing them out of concerns for safety and hygiene, among others. But for the first time in Europe, such fecal transplants have been endorsed as a recommended treatment for the infections, as outlined in new guidelines from the National Institute for Health and Care Excellence, a U.K. body.

Infections of C. difficile are among the most common in hospitals and can result from prolonged use of antibiotics. They cause patients enormous distress, including severe diarrhea that can lead to dehydration and other complications that make recovery from surgery difficult. Cases have been proliferating in Europe, and new antibiotic-resistant strains are emerging as well, according to data from the upcoming United European Gastroenterology Week meeting in Austria.

The infection is notoriously hard to treat, and if the standard first-line therapies of targeted antibiotics fail, patients and their doctors are willing to try anything to shut down the rampant growth of bacteria. Enter the fecal transplant, which involves doctors taking feces donated by a generous healthy stranger (who doesn’t harbor C. difficile or other infections), liquefying it in a solution of saline, water, or even milk or yogurt, straining it and delivering the resulting solution to another patient via colonoscopy. People generally feel better just a couple days after the transplant, and many recent studies show the treatment cures around 90% of C. difficile infections.

There’s little question that it works, but only a few facilities, including the Mayo Clinic in Arizona, perform fecal transplants in the U.S. because it isn’t standardized yet. Though Mayo Clinic screens donors for months through blood and stool tests, for example, not everyone does. “You don’t really know what’s in this concoction that you’re putting into somebody, and the FDA really doesn’t like that,” says Robert Orenstein, associate professor and chair of the division of infectious diseases at Mayo Clinic in Arizona, which began the performing the procedures in 2011, and now attracts patients from all over the world for the treatment.

MORE: The Latest Thing From Pills? Ones Made from Poop

Another cause for concern: there’s no long-term safety data. “It’s assumed that manipulation of the gut flora may have a lot of other downstream effects,” says Orenstein, like affecting inflammatory or metabolic diseases like diabetes. “Nobody knows that if you took the microbiome from one individual and placed it into another, whether some of these things might evolve.”

Though his facility has performed about 120 fecal transplants so far, Orenstein still calls the procedure “medieval.” Instead of relying on the physical swapping of fecal samples, for example, he anticipates that if the research on the role that microbes can play in our health continues, we may soon have microbiota pills—super-evolved probiotics, basically—that will recolonize places like the gut or respiratory tract with the right microorganisms. “We’re just in the beginning,” he says. “In a couple years, we’ll have almost all of this figured out.” In the meantime, we can learn from Europe’s example—and hope that those pills come soon.

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