Probiotics and Microorganisms

There are differences in the intestinal microbiota (microorganisms that live in the digestive tract) in IBD patients as compared to those without IBD. Those with IBD have less microbial diversity and a loss of beneficial and anti-inflammatory bacteria.


Good bacteria are beneficial because they keep the harmful bacteria in check. If the balance between the two is thrown off, harmful bacteria may overgrow causing diarrhea and other digestive problems. That’s where probiotics come in.


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Complementary Medicine for IBD: Probiotics and Microorganisms


Probiotic therapy

The World Health Organization (WHO) defines probiotics as, “live microorganisms, which when consumed in adequate amounts confer health and benefit to the host.”


Probiotics are used to restore the balance of these “good” bacteria in the body. They are generally safe with few potential side effects, such a gas or bloating. As with any new complementary treatment, it’s important to talk to your doctor about before starting probiotics, especially if you are a young child, older adult, or have a compromised immune system.

Sources of probiotics

  • Dietary supplements, including capsules, tablets, and powders
  • Yogurt
  • Kefir
  • Miso
  • Tempeh

You can also take probiotics in capsule form.


Studies on probiotics are limited. In ulcerative colitis, studies suggest there may be a benefit at inducing and maintaining remission. In Crohn’s disease, studies are also limited, but prevention and remission has not been associated with taking probiotics.


In pouchitis, studies suggest there may be a benefit in preventing and maintaining remission. Always talk with your provider before starting any probiotic therapies.


Gionchetti P, Rizzello F, Morselli C, et al. High-dose probiotics for the treatment of active pouchitis. Dis Colon Rectum. 2007;50:2075-2082.

Fecal microbiota transplantation

Fecal microbiota transplantation (FMT) is a procedure in which fecal material is transferred from a healthy individual (donor) to patient with alteration in normal microbiota (recipient).


Although it is effective for the treatment of recurrent Clostridioides difficile (C-Diff) infection, further research is needed to determine if it is an effective treatment for IBD. Some studies suggest that FMT has the potential to induce remission in mild-to-moderate ulcerative colitis. It is not permitted by the FDA for treatment of IBD at this time, but many clinical trials are underway. If you are interested in learning more about a trial, we strongly recommend that you consult with your healthcare provider about the trials that may interest you.

Mycobacterium avium paratuberculosis (MAP)

Mycobacterium avium paratuberculosis (MAP) is a bacteria that is being studied and may have a relationship to Crohn’s disease.  The MAP bacteria are more frequently recovered from the intestines of patients with Crohn's disease compared to ulcerative colitis or healthy individuals.  


Multicenter studies treating Crohn’s disease patients with a combination of anti-MAP antibiotics are ongoing. Many researchers discount MAP as a cause of Crohn's disease; however, more research is needed.