The bacteria that live in our healthy guts are a garden of cooperating and competing species that help to determine our intestinal health. When we take antibiotics, we kill countless bystander bacteria in our guts and sometimes develop changes in our digestion which can be severe. Clostridium difficile infection is one of these conditions, a superinfection with a bacterium which is pretty resistant to antibiotics and causes infection of the colon with diarrhea, sometimes fever, nausea and vomiting and occasionally death. We treat Clostridium difficile (C. diff) diarrhea with a couple of antibiotics to which it is sensitive, but they don’t work very well and some patients become chronically infected.

What does work for C. diff, when all else fails, is a fecal transplant, that is to say taking stool from a healthy person and putting it into the gut of a person who has the infection. This is a stinky procedure in which genuine human poop, from a human who has been tested for diseases like HIV that can cause their own problems, is diluted with saline and instilled into the gut either with a colonoscopy, a naso-enteric tube or a simple enema. It works quickly, like in one or two days and the patient, once cured, usually stays cured. It doesn’t work on every single person, but very nearly.

Various physicians around the country do real fecal transplants, but it is surprisingly difficult to find a doctor who will. I saw a successful fecal transplant at our office a few years ago which was, in fact, very easy and instantly rendered the recipient well. The poop was mixed to a liquid consistency in a blender with saline and instilled by enema into the patient with the chronic C. diff.

Researchers from Canada recently reported the successful treatment of two patients with Clostridium difficile diarrhea with a combination of 33 bacteria isolated from the stool of a single healthy woman.  They tested an original group of over 60 bacteria for antibiotic resistance and chose the bacteria that did not appear to have any significant levels of resistance. The bacteria colonized the recipients’ guts after being introduced by a tube into the duodenum from the nose, and the two patients, who had recurrent severe C. diff infections, were symptom free 24 and 26 weeks after the procedure, despite being treated with antibiotics for other infections (which often leads to relapse in conventionally treated patients.) It sounds like these researchers have created an excellent human derived probiotic, but I’m thinking that if fecal transplant is actually successful, it makes sense to consider doing real fecal transplants with real feces, which will never cost very much and are much more diverse as far as bacterial species are concerned. The artificial poo extract is more likely to be adopted as standard of care, though, because it is not brown and stinky and will eventually be backed by a major pharmaceutical company.

Patients die frequently in the hospital as a result of C. diff infection. Because fecal transplants are so yucky that nobody wants to even discuss them, much less perform them, we allow many people to die every year of colitis due to C. diff. It is difficult to imagine that our cultural aversion to the products of our lower intestines regularly results in patients actually dying. A study in the New England Journal of Medicine reported this month was stopped early by the institutional review board in the Netherlands because fecal transplant was so much more effective than antibiotic therapy that continuing to offer patients the inferior option was considered unethical. For a good long while it will continue to be ethical to offer only antibiotic therapy for C. diff at American hospitals, and to not even discuss fecal transplants except perhaps as a way to make physicians and nurses squirm.

It is clear that intestinal bacteria populations are responsible for more than making us poop regularly. Fecal diversity is related to weight gain in mice, for instance. Fecal transplants have been used successfully to treat inflammatory bowel disease such as ulcerative colitis. I’ve wondered if the spreading epidemic of gluten intolerance has to do with the huge amounts of antibiotics that humans in the US are prescribed and if that, too, might be treated with repopulation of the gut with the diverse collection of bacteria that make up the feces of healthy and ideally antibiotic naive people (if there are any of those left.) It seems to me that widespread antibiotic use in our communities in general has probably significantly affected the bacteria in all of our guts, even those of us who rarely or never take them. Antibiotic use in food animals probably contributes as well to a shift in our normal flora. Perhaps some of this recent research will push us to begin to venerate our bacterial symbionts and strongly consider their well being when considering taking or prescribing antibiotics.

Janice Boughton is a physician who blogs at Why is American health care so expensive?