The bacterium Clostridium difficile (also known as C. diff) is a major pathogenic contributor to the development of antibiotic-associated diarrhea, or diarrhea that results from taking an antibiotic. According to the Centers for Disease Control (CDC), C. difficile diarrhea is linked to 14,000 deaths in the United States each year.1 Interestingly, first line treatment for C. diff infection is antibiotics—the very medicine that triggers the infection in the first place. This might explain why the relapse rate for C. diff infection is 20–35 percent.2 That is, 20–35 percent of people who get C. diff once will get it again. It’s a vicious cycle of intestinal imbalance.

One specific strain of C. diff—PCR ribotype 027, or C. diff 027—is particularly responsible for the C. diff epidemics in North America and Europe. C. diff 027 produces a high level of toxins3 and is associated with high rates of recurrence, hospital outbreaks, and death.4 In a recent study published in the Public Library of Science Pathogens journal, researchers used an animal model of C. diff 027 infection to determine its relation to gut bacterial imbalance, or dysbiosis, during treatment with antibiotics and bacteriotherapy,5 or the use of beneficial bacteria to displace pathogenic bacteria.6

According to the researchers, “Persistent infection is linked to intestinal dysbiosis that can be resolved by restoring a diverse intestinal microbiota with bacteriotherapy using a defined, simplified mixture of intestinal bacteria.” Now we’re getting somewhere.

This highlights the difference between integrative, or functional, medicine and conventional, or allopathic, medicine. Allopathic medicine seeks to treat disease with a silver bullet, usually a drug that targets one specific symptom or sign—in the case of C. diff, antibiotics are the silver bullet. This tunnel vision method of medicine often misses the forest for the trees, however. Integrative medicine, however, seeks to understand the details of disease, but within the context of the larger picture that takes into account a broad range of factors. Allopathic medicine treats C. diff infection with a medication known to cause the infection in the first place. This clearly does not take into account the larger picture.

This new study is more aligned with integrative medicine principles. These researchers are building on recent advances in bacteriotherapy that are particularly exciting. Fecal bacteriotherapy, or fecal transplant, involves the transfer of fecal bacteria from a healthy individual to an individual with illness—in this case, to an individual with C. diff. This treatment has been reported to have an average success rate close to 90 percent.7,8 Despite the amazing results seen so far with fecal transplant, finding a suitable healthy donor can be time consuming, there is a risk of inadvertently introducing opportunistic pathogens, and frankly, many people don’t like the idea of receiving a transplant of someone else’s poop—healthy or not, family member or not. It’s unfortunate, but it’s true.

For these reasons, the researchers of the PLoS study sought out the specific bacteria from fecal transplants that were found to promote the growth of “health-associated commensal bacteria that appear to be suppressed during persistent dysbiosis and the subsequent displacement of epidemic C. difficile.” Using an animal model, they found six bacteria—three known bacteria, and three novel, or previously unidentified, species that best inhibited C. diff. These six bacteria represent a diverse mix, both obligate and facultative anaerobic bacteria that represent three out of four predominant intestinal groups.

More studies are needed to determine what other strains may be helpful against C. diff, and whether these strains work as well in humans as they do in the animal model. The authors of the study sum it up nicely, “Following these principles we believe that it is likely that many distinct combinations of bacterial strains will have the potential to treat recalcitrant or recurring C. difficile infection. These observations open the way to rationally harness the therapeutic potential of health-associated microbial communities to treat recurrent C. difficile disease and transmission in humans, and potentially other forms of disease-associated dysbiosis.”

This research helps to lay the foundation of the future. I believe we will soon see specific bacteriotherapies for conditions such as ulcerative colitis, Crohn’s, morbid obesity, metabolic syndrome, diabesity, autoimmune disease, and neurodegenerative/inflammatory diseases ranging from Alzheimer’s and Parkinson’s to autism spectrum disorder. In the meantime, balance your gut with a multi-strain probiotic that resembles the great diversity found in a healthy digestive tract.


  2. E.J. Kuipers and C.M. Surawicz, “Clostridium difficile infection.” Lancet. 2008 May 3;371(9623):1486–8.
  3. M. Warny, et al., “Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe.” Lancet. 2005 Sep 24-30;366(9491):1079-84.
  4. L.C. McDonald, et al., “An epidemic, toxin gene-variant strain of Clostridium difficile.” N Engl J Med. 2005 Dec 8;353(23):2433-41.
  5. P. Huovinen, “Bacteriotherapy: the time has come.” BMJ. 2001 August 18; 323(7309): 353–354.
  6. J.S. Bakken, “Fecal bacteriotherapy for recurrent Clostridium difficile infection.” Anaerobe. 2009 Dec;15(6):285-9.
  7. M.J. Hamilton, et al., “Standardized frozen preparation for transplantation of fecal microbiota for recurrent Clostridium difficile infection.” Am J Gastroenterol. 2012 May; 107:761.
  1. T.D. Lawley, et al., “Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice.” PLoS Pathogens. 2012 October;8(10):e1002995.