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Fecal Microbiota Transplant for Ulcerative Colitis, IBS and more

Updated: Dec 7, 2023

Healing Ulcerative Colitis, Crohn and more Through Donor Microbes

Fecal Microbiota Transplant (FMT) has emerged as a revolutionary approach to address various gastrointestinal disorders by leveraging the power of healthy gut microbes. This video explores the history, applications, protocols, and considerations surrounding FMT, shedding light on its potential to treat certain gastrointestinal conditions. In this interview, Dr. Mary talks with Dr. Scheeler, who specializes in the use of FMT for the treatment of inflammatory bowel disease (IBD).

Notes from this interview:

What is FMT?

Fecal Microbiota Transplant (FMT) is taking the stool from a healthy person and transplanting that to another individual, who has a gastrointestinal condition, with the goal of reintroducing beneficial organisms into the gut.

History of FMT

The practice of FMT dates back centuries, with its origins rooted in traditional medicine. From the Chinese physician Ge Hong's "Yellow Soup" in the 4th century to the 17th-century use in veterinary medicine, FMT has evolved into a modern medical intervention.

FMT for C. diff Infections

FMT's efficacy in preventing or treating treatment-resistant C. difficile (C. diff) infections led to its initial recognition by the FDA. FMT is currently only approved by FDA for the prevention of the recurrence of Clostridioides difficile infection. Products like Rebyota and Vowst have gained FDA approval for this purpose, marking a significant advancement in gastrointestinal medicine.


The correlation between gut flora and inflammatory responses in genetically susceptible individuals has driven research into FMT's potential for treating inflammatory bowel disease (IBD). Studies have shown promising results, with remission rates of around 25-35% in FMT intervention groups compared to 8-10% in control groups.

Key Studies that Dr. Scheeler discussed:

  • Moyaeddi et al. (2015): Weekly FMT in patients with ulcerative colitis over 6 weeks demonstrated superior outcomes in achieving endoscopic remission compared to a group who received water enemas.

  • Rossen et al. (2015): The TURN trial explored nasoduodenal tube transfers for FMT, in patients with mild to moderate ulcerative colitis. The study findings hinted at higher remission rates in the FMT group. It is important to note that the study did not meet statistical significance.

  • Paramsothy et al. (2017): A randomized controlled trial in patients with ulcerative colitis who had a Mayo score between 4-10. Patients received either FMT or placebo colonoscopic infusion, followed by enemas 5 days per week for 8 weeks. Clinical remission and endoscopic response was achieved in 11 (27%) of 41 patients allocated to FMT versus three (8%) of 40 who were assigned placebo.

  • Costello et al. (2017): A randomized controlled trial, 73 adults with mild to moderately active UC. They received either anaerobically prepared pooled donor FMT (FMT was from multiple donors) or autologous (stool from the patient themselves) FMT (n = 35) via colonoscopy followed by 2 enemas over 7 days. Steroid-free remission was achieved in 12 of the 38 (32%) receiving pooled donor FMT compared with 3 of the 35 (9%) receiving autologous FMT.

FMT in Crohn Disease (CD)

A recent meta-analysis suggests that FMT can induce remission in CD patients, with around 57% achieving clinical remission within weeks. However, endoscopy results have shown mixed outcomes.

FMT in Irritable Bowel Syndrome (IBS)

Dr. Scheeler discussed how three double-blind, placebo-controlled studies have been done on the use of FMT in IBS, one showed no effect and two had positive findings.

  • The one that showed no effect was using oral capsule FMT. The two studies with positive findings were delivered by gastroscope or colonoscope.

  • Johnsen et al studied subjects with IBS-M and IBS-D who had moderate to severe IBS. FMT was administered by a colonoscope. 36 (65%) of 55 participants receiving active treatment versus 12 (43%) of 28 receiving the placebo showed response at 3 months (p=0·049).

  • The most recent, largest study completed in 2019 showed that positive responses occurred in 23.6%, 76.9% (p<0.0001) and 89.1% (p<00.0001) of the patients who received placebo, 30 g FMT, and 60 g of FMT respectively. Positive outcomes were observed when delivered via gastroscope or colonoscope, indicating potential for symptom relief but more research is needed.

FMT in Small Intestinal Bacterial Overgrowth (SIBO)

A randomized control study from China showcased significant improvement in gastrointestinal symptoms for SIBO patients following FMT treatment compared to a placebo group. 55 patients with SIBO were enrolled, so it was a small study. Subjects either received FMT capsules once a week for 4 weeks or placebo capsules. Gastrointestinal symptoms significantly improved in SIBO patients after treatment with FMT compared to participants in the placebo group, and the gut microbiota diversity of FMT group had a significant increase but again more research is needed since the research is still limited for SIBO.

The FMT Protocol

The FMT process involves collecting stool from rigorously screened donors, blending it with filtered water or saline, straining out particles, and introducing it into the colon through retention enema, colonoscopy or occasionally endoscopy. Multiple treatments are commonly employed for conditions like IBD.

Donor Screening

Donor screening is vital to prevent the transmission of infectious diseases. A comprehensive screening includes blood and stool tests, covering various pathogens. Even young children should be tested due to susceptibility to colonization of C.diff.

Pros and Cons

Prospective donors should be generally healthy, with regular bowel movements and a microbiome-supportive diet. However, risks include potential complications from insertion procedures and transient side effects like abdominal pain, diarrhea, and bloating. The major concern is transmission of infection from the donor stool to the recipient which is why donor screening is imperative but is also not foolproof since every disease can not be screened for. There have been deaths noted when the recipient was immunocompromised and an infection was transmitted by the donor but this is rare.

FMT Products new to the market

FDA-approved products like Rebyota (rectal administration) and Vowst (oral administration) are only approved for the treatment of recurrent C. diff infections, they have not been approved for the treatment of IBD yet.


Fecal Microbiota Transplant represents an exciting approach to addressing various gastrointestinal disorders by restoring healthy gut flora. With every treatment, there are risks and benefits and it's crucial to discuss those with a qualified health care practitioner. Dr. Scheeler does not use FMT as a first line treatment for most conditions and believes that we are still in the early stages of research around this promising area of study.

If you would like to become a patient with Dr. Natalie Scheeler, visit the link below:


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