Warning: Here comes the icky diarrhea blog.  Because I primarily write about microbiota, this was only a matter of time as the literature is replete with gut microbiota studies.  This abundance is due to lots of money being poured into figuring out the role of the gut microbiota; they are likely to influence a plethora of diseases through their role in immune system development, and fecal samples are easy to obtain!

Fecal samples are also relatively easy to transplant.  This may sound gross beyond belief, but transplantation of fecal material actually works to restore health to those suffering from antibiotic-induced chronic diarrhea.  We don't know exactly why it works, or the exact problem it is treating, but it saves lives and therefore deserves attention.

The gut microbiota is a diverse milieu of bacteria (and other microbes) that are constantly walking a tight-rope with the immune system.  It is impossible for the immune system to kill all these bacteria, and it is known that interactions between immune cells and bacteria guide proper development of immunity.  The bacteria, on the other hand, have a relatively nutrient-rich environment so long as they stay where they should.  So, humans and their microbes live in a sort of equilibrium: the human host gets a properly developed immune system for use against the worst of pathogens (in addition to the digestion of food), and the bacteria get a warm nutrient-rich environment.  The bacteria that help in this immune system development are also considered beneficial because they keep unwanted pathogens at bay.  There is a complicated ecosystem functioning here, where bacterial species are also keeping each other in check.  We're really only beginning to tease apart these complex interactions.

This is the hypothesis underlying the success of fecal transplantation.  Patients with chronic antibiotic-induced diarrhea often have intestines infected with a particularly virulent strain of Clostridium difficile.  Although C. difficile is also commonly found in healthy intestines, it is thought that the other microbes prevent it from causing problems.  But once the antibiotics have killed many of these beneficial bacteria, nothing stands in the way of antibiotic-resistant C. difficile wreaking havoc.

Enter fecal transplantation.  Adding back the beneficial bacteria that were killed by antibiotics is the best way to restore balance in the intestines, thereby eliminating C. difficile, or its ability to cause harm.  But we don't yet know which species of bacteria is (are) beneficial, and it is likely that there are multiple species perhaps reliant upon each other for the beneficial effect. The addition of gut microbiota from a healthy person (contained in their feces) restores the balance of the microbes in the intestines.

How will we figure out which bacteria are the good ones, restoring the balance and fighting off harmful C. difficileOne recent effort by Shahinas et al. has helped narrow this down a bit, by comparing the communities of bacteria in feces from the healthy donors, the pre-transplanted patients, and the post-transplanted patients.  Bacteroidetes and Firmicute bacteria increased in abundance after transplantation, mirroring the communities from healthy donors.  The community compositions of the transplants were not completely similar to those from healthy donors, but were "healthy" enough to rid the patients of diarrhea symptoms.

Bacteroidetes and Firmicutes are phyla with a vast number of species (C. difficile is a member of Firmicutes).  Which species are responsible for the health of the intestines?  How many are there?  Do they work together in synergy?  How do they prevent C. difficile
induced diarrhea under healthy conditions?  Will we one day be able to provide patients with a pill rather than a fecal transplantation?  Hundreds of scientists around the world are working on these very problems.  Soon enough the answers will be ours.