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Will Fecal Microbiota Transplantation Work for Crohn’s Disease?

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Will Fecal Microbiota Transplantation Work for Crohn’s Disease?


image of man with Crohns

Note: If you haven’t read it, you may be interested in this comprehensive article on Crohn’s Disease and Diet.

Fecal microbiota transplantation (FMT) involves the replacement of the entire population of dysfunctional gut bacteria (gut microbiome) with healthy bacteria from healthy donor stool. The technique has been incredibly successful (90-98%) and safe for treating C diff infections caused by the bacteria Clostridia difficile. The question on everyone’s mind is what else can this procedure be used for. Clearly, conditions involving gut dysbiosis (unbalances in intestinal bacteria) make sensible targets. Early reports are promising for treating the other inflammatory bowel disease, ulcerative colitis, but what about Crohn’s disease?

Crohn’s disease is an inflammatory bowel disease (IBD) that affects approximately 600,000 people in the US.

[i] People who have Crohn’s suffer from a serious inflammation or irritation of their digestive tract which can lead to sores or ulcers forming, particularly near the end of the small intestine (called the ileum). The small intestine is where critical nutrient absorption takes place, so people with Crohn’s often don’t digest and absorb nutrients well. This can result in malnutrition, anemia and malabsorption of key vitamins and minerals such as vitamin B12, vitamin A, vitamin D, Vitamin E, vitamin K, folate, zinc, calcium and iron. The most common symptoms of Crohn’s include:

  • Severe watery diarrhea
  • Intense abdominal pain or cramping
  • Weight-loss
  • Fever
  • Fatigue

Despite extensive research, the exact cause of Crohn’s disease remains unknown. People with Crohn’s have various mutations (NOD2, ATG16L1, IL-23, IL12B, STAT3 and NKX2-3) in their genes that healthy people don’t have. Expression of the altered genes affects how bacteria interact with the intestinal surface and how our immune system interacts with these adherent bacteria.[ii] An imbalance in intestinal bacterial developing in response to the genetic abnormalities present in Crohn’s, may be the trigger for damaging inflammation characteristic of Crohn’s disease.

One thing is clear – People with Crohn’s have an altered microbiome suffering a 50% decrease in the diversity of gut microbes including the loss of bacterial species Bacteriodes, Eubacterium and Lactobacillus.[iii]A separate study also observed depletion of commensal bacteria, notably Firmicutes and Bacteroidetes bacterial types.[iv] A third study observed a decrease in Bacteroides bacteria and a decrease in bacterial end products. These studies point to a significant imbalance or gut microbes in people with Crohn’s disease. This imbalance may help explain the higher incidence of Clostridia difficile infection in people with inflammatory bowel disease.[v]

According to this CBS Boston News article, Dr. Alan Moss, Associate Professor of Medicine at Harvard Medical School and Beth Isreas Deaconess Medical Center is leading the effort to see if fecal transplantation can help people with Crohn’s disease. Though the results from this ongoing clinical trial are not available, one of the patients in the study had this to say: I see this as a major breakthrough in medicine by treating patients naturally, and it makes perfect sense. I’ve been eating and drinking whatever I want, and the Crohn’s symptoms I typically would have at this time are either minimal or nonexistent—symptoms such as sharp pain in my colon, cramps, bleeding ulcers, lethargy, joint pain, and diarrhea.”

Whether or not this treatment will work for Crohn’s, and how long the benefit will last are open questions, but there is reason to be optimistic.

[i] Kappelman MD, Moore KR, Allen JK, Cook SF. Recent trends in the prevalence of Crohn’s disease and ulcerative colitis in a commercially insured US population. Dig Dis Sci. 2013 Feb;58(2):519-25.

[ii] Podolsky DK. Inflammatory bowel disease. N Engl J Med. 2002 Aug 8;347(6):417-29.

[iii] S J Ott, M Musfeldt, D F Wenderoth, J Hampe, O Brant, U R Fo¨lsch, K N Timmis, S Schreiber. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 2004;53:685–693.

[iv] Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13780-5.

[v] Navaneethan U, Venkatesh PG, Shen B. Clostridium difficile infection and inflammatory bowel disease: understanding the evolving relationship. World J Gastroenterol. 2010 Oct 21;16(39):4892-904.

Note December 3, 2014: To Track this study, check out this link.

By |2016-11-05T04:26:24+00:00November 5th, 2013|Crohns Disease, Fecal Transplants, Ulcerative colitis|19 Comments

About the Author:

Norm Robillard received his Ph.D. in microbiology from the University of Massachusetts, Amherst studying Bacillus anthracis and other Bacillus species. His post-doctoral training at Tufts University focused on antibiotic resistance and gene transfer between the gut microbes Bacteroides fragilis and E. coli. During his career in pharma / biotech, Dr. Robillard studied the genetics of antibiotic resistance, septic shock, viral illnesses and antimicrobial and antibody-based therapies prior to founding the Digestive Health Institute. Dr. Robillard is the creator of the Fast Tract Diet, author of the Fast Tract Digestion book series and publisher of the Fast Tract Diet mobile app. He was the first to propose excess intestinal fermentation as the underlying cause of acid reflux and explained the connection between intragastric pressure from gas-producing bacteria in our intestines, nutritional malabsorption and the symptoms of acid reflux. His latest book series, Fast Tract Digestion provides a safe and effective dietary tool and behavioral strategy as an alternative to proton pump inhibitors (PPIs), H2 blockers, IBS drugs or antibiotics for heartburn, acid reflux, GERD, laryngopharyngeal reflux disease (LPR), IBS and other SIBO related conditions.


  1. Danny J Albers November 6, 2013 at 12:16 am

    Good news to be sure anxious to see the full trial results.

    • Norm Robillard November 6, 2013 at 12:35 am

      For sure Danny. And will any improvement be lasting? My gut says you won’t be able to eat what ever you want regardless.

  2. Elle March 19, 2014 at 2:56 am

    Do you think that FT could be a cure for SIBO too?

    • Norm Robillard March 19, 2014 at 3:35 am

      Hi Elle,
      Probably not a cure if the underlying cause(s) are not addressed. Fast Tract Digestion covers these underlying causes and how to address them. It would most likely make a big improvement though. The reason it cures C. diff. is because you have single species of bacteria, normally not present in most people’s gut in high numbers. Once you get rid of it, you’re fine if you don’t get re-infected.

  3. Anne Amigo April 5, 2014 at 2:09 am

    Is there any evidence that using healthy family fecal matter for transplant is superior for Crohn’s disease?
    Have another patient with chronic there any evidence FT could help her?
    Thank you Norm,
    Anne ,family physician Sydney

    • Norm Robillard April 5, 2014 at 3:15 am

      Hi Dr. Amigo, Thanks for two interesting questions. Sorry, I don’t know of any work at all specifically employing fecal matter from a family member for transplantation in Crohn’s. Nor have I heard of FMT testing for constipation, though intuitively it makes some sense at least in cases where constipation is linked to methane-positive breath testing indicative of M. Smithii overgrowth.

  4. Mother of Crohn's Teen May 8, 2014 at 8:29 am

    I would love you to read my son’s story! He was diagnosed with widespread Crohn’s Disease just before he turned 13. He is now 16 and has had over 130 FMT enemas. He has been off imuran since February 2013 (15 months) and has absolutely no sign whatsoever of Crohn’s Disease, clinically, or histologically. His doctor is Professor Borody, a pioneer of FMT.

    Part 1

    Part 2

    • Norm Robillard May 8, 2014 at 11:32 am

      Hi Mom,
      Thank you for posting. I just read your amazing story of your son’s extended remission through FMT. I met Dr. Borody last year at a meeting in the states. He is truly a pioneer and a big reason FMT has gained so much attention for treating conditions other than C. diff infection, but success stories like your own drive home the importance of pursuing more studies using this procedure for Crohn’s. I hope your son will be able to remain free of Crohn’s for life with this strategy.

  5. Mother of Crohn's Teen May 9, 2014 at 4:32 am

    I agree Norm, studies are definitely needed – and I hope they aren’t short term studies where they use FMT for say a couple of treatments. I think one of the keys to success is long term FMT for Crohn’s Disease (it seems to be more stubborn)… then of course there’s the important question who makes a good donor? A donor’s microbiota may not work at all if they don’t have the diversity or specific organism needed to reverse Crohn’s – and this is something that needs unravelling! A great piece on Prof. Borody, FMT and Crohn’s Disease featured on the news in Australia recently It’s very exciting to be part of the forefront in the revolution of medicine!

  6. Norm Robillard May 9, 2014 at 1:23 pm

    Thanks Mom, Just watched. Very exciting possibilities.

  7. Crohn's Sufferer May 29, 2014 at 7:26 am

    This seems very promising. I am actually meeting w/ a doctor next month to explore this very treatment. I have been living w/ CD for 20 years now (I am 36 yr old male) and it has held me back in life in several ways…. I am cautiously optimistic.

  8. Robert Brown September 9, 2014 at 3:08 pm

    I suffer from what is described as Chrons disease. I am interested in at least trying a fecal transplant. Are there other countries doing this? Are there experimental programmes I could be involved with? Desperate to salvage some of the life I have left.

  9. Gina Plageman October 18, 2014 at 4:19 pm

    Has anyone one with crohn’s had the fecal transplant who had surgery before?

    • Gina Plageman October 18, 2014 at 4:19 pm

      Prior colon surgeries?

  10. Tee Woo October 18, 2014 at 7:54 pm

    I have Crohn’s disease but my GI doctor refuses that treatment. I live in NJ but I am not sure how to find a doctor that will treat me with this. Any website I could use to find one? I am desperate. I do not believe on being on so many drugs to to take care of the symptoms.

    Thank you,


  11. sean December 3, 2014 at 6:34 pm

    Any results published from that trial yet?

    • Norm Robillard December 3, 2014 at 7:12 pm

      Good question Sean. I looked for an update on They are no longer enrolling and had planned to have all the data as of Sept 2014. Not sure when the results will be published. I added a link at the bottom of the article for people who want to check on the study for updates.

  12. Donna Ward March 17, 2015 at 4:05 pm

    My son has Crohn’s and now has c-diff. Would love to find a doctor in my area or within driving distance that would be willing to use FMT instead of the Remicade and imuran. If anyone know one near Alabama please post. Or email me @

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