• Fecal Microbiota Transplant (FMT) is the act of transferring stool from a healthy donor into the gut of someone who has certain health conditions.
  • It can be done at home with the guidance of a doctor or healthcare professional who will be able to assist with screening, equipment and advice.
  • Side effects are uncommon and it is a safe procedure provided the donated sample is screened appropriately and the procedure is done correctly.
  • Research shows that it is very effective in C. diff infections, and may help in IBD.
  • Latest study found that using anaerobic donor specimens (bacteria that had not been exposed to air) may be more effective.

Truly Natural Healing of Your IBD

Metronidazole (Flagyl), Ciprofloxacin, Cyclosporine, Infliximab, Prednisone, and my favorite moniker, Dexpak Taperpak, are all long and complex names for drugs that many of you may be familiar with. You might not know what they mean exactly, and you might only have a vague understanding of what they are doing to you, but you’ve probably seen or heard, and possibly struggled to remember how to properly pronounce many of them.

There’s a different simple and natural option for treatment that many of you should consider called fecal microbiota transplant (FMT), also known as a stool transplant. FMT is the gradual replacement of bad bacteria in your gut with healthy bacteria from a healthy gut, through the medium of feces, or in common parlance: Poop.

Fecal matter is one of the most natural compounds on Earth, and much easier to remember and pronounce than the names of mostly synthetic drugs. It literally returns to the earth when breaking down and eventually becomes soil, which facilitates the growth of plants to be consumed by animals before being deposited in the earth where it all started. I’ll bet Elton John wasn’t thinking about that when he wrote Circle of Life.

And on that note, poop is not only one of the natural roots of our planet, it’s one of the natural roots of our humor. So, it’s fitting that the first appearance of fecal microbiota transplant for humans in western history starts with the Germans.

During World War Two, German soldiers in North Africa found themselves suffering from dysentery in response to the conditions of food and water in their new desert biome. The Bedouins, a nomadic desert people, introduced them to a local remedy. They fed them fresh, warm camel feces. Just like many people who have found success treating their IBD and IBS with FMT, the soldiers found that poop was much easier to stomach than constant pain.

Fecal microbiota are free, natural and a part of everyday life. It is a medical therapy that is available from licensed health care providers, but if it is not covered by your insurance for Crohn’s or UC, it is possible to DIY this therapy and many people do perform it themselves at home. It’s considered to be highly effective and over ten thousand procedures have been performed since its induction into western medicine in 1958.1

What is FMT?

Fecal microbiota transplantation (FMT) is the administration of a solution of fecal matter from a donor into the intestinal tract of a recipient in order to directly change the recipient’s microbial composition and confer a health benefit.

Fecal Microbiota Transplantation: In Perspective; Shaan Gupta, Emma Allen-Vercoe, and Elaine O. Petrof

Over half of our body is made up of microbes that are working for us, but not actually a part of us. Each of us have our own unique microbiota. It’s a lot like a fingerprint. We don’t completely understand this biome yet and our microbes have inspired a huge amount of studies which have linked them to a seemingly endless list of health problems and conditions. Obesity, diabetes, autism, dandruff, alopecia universalis, diarrhea, cancer, depression, colitis and Crohn’s, these are just some examples of conditions that could potentially be cured by FMT. Our body’s bacteria boosts the immune system, metabolism, crucial hormones – and the list goes on. Anyway, it’s becoming increasingly clear that the study of our microbes will have stunning potential for treatment of all kinds of things.2 But we’re just here to talk about pooping.

There is a current consensus in literature that IBD is very likely caused by a genetic predisposition to an unusual immune response to certain bacteria (endoluminal). Certain bacteria have been shown to alter the development of anti-inflammatory T-regulatory cells and proinflammatory cells. The composition of microbiota have been noted to shift in patients with IBD, who have less diversity in their luminal microbiota. Since IBD is closely associated with unusual microbiota, it’s natural to investigate FMT as a treatment.

FMT has shown varying success rates for IBD, with the most recent study reporting improvements in one third of patients.3 An infusion of healthy bacteria from someone else’s poop could heal your gut.

Bonus Even the television show “Grey’s Anatomy” gives an explanation of FMT.

What Do The Studies Show?

Clostridium difficile (C. diff) infections

In the last two decades, FMT has been the subject of a huge amount of study because it’s an effective and safe cure for C. diff, a bacterium that can cause problems ranging from diarrhea to life-threatening inflammation of the colon. It’s also become unexpectedly hip as a potential therapy for gluten intolerance. One IBD patient who reported success with FMT referred to the expanding field as the “wild-west.”

In February of 2018, the IDSA/SHEA released Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children. Of all treatments for both first and second recurrence of C. diff, FMT is the only strongly recommended technique and one of two with “moderate” support for its effectiveness.

As most studies concentrate on C. diff, there is less direct research on FMT for IBD or IBS. But the research on C. diff is extremely notable because patients with IBD are at increased risk and impact of C. diff. The probability of contracting C. diff within five years of being diagnosed with UC is potentially greater than 3% and then increases the risk of colectomy, post-op complications, and death due to the dual conditions. IBD sufferers are also 33% more at risk of recurrence of C. diff. These risks are further amplified for those suffering specifically from ulcerative colitis.

FMT effects on IBD

A 2012 paper, Systematic Review: Faecal Microbiota Transplantation in the Management of Inflammatory Bowel Disease found nine articles, documenting 26 patients. 17 of the 26 patients reported results, 13 of 17 patients were able to discontinue all IBD medication within six weeks, and all 26 had symptoms reduced or resolved after four months.

A 2015 paper, Fecal Microbiota Transplantation: A Review of Emerging Indications Beyond Relapsing Clostridium Difficile Toxin Colitis, did not go as far as to state an absolute conclusion, but did find generally positive research results. However, they noted that one study found negative results. They

…analyzed the bacterial colonies present both pre- and post-FMT in 5 patients with severe to moderate ulcerative colitis. In contrast to previous reports, none of the five patients achieved a remission by 12 weeks. Furthermore, only one of the five experienced a response, whereas two patients experienced further clinical deterioration of their condition at four weeks post-FMT.

Temporal Bacterial Community Dynamics Vary Among Ulcerative Colitis Patients, After Fecal Microbiota Transplantation

Children with C. diff have been shown to experience less success, but a 2013 study, Safety, Tolerability, and Clinical Response After Fecal Transplantation in Children and Young Adults with Ulcerative Colitis, studied nine children with UC, ages 7 to 21. Seven showed a positive response within one week, six at one month, and three experienced clinical remission within the first week.

Another paper concluded that,

While C. difficile is easily eradicated with a single FMT infusion, this generally appears to not be the case with ulcerative colitis. Published experience of ulcerative colitis treatment with FMT largely shows that multiple and recurrent infusions are required to achieve prolonged remission or cure.

Fecal Microbiota Transplantation: Current Status and Future Directions

Most recently, an Australian study Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis: A Randomized Clinical Trial. found optimistic results when using short term FMT in patients with ulcerative colitis. They specifically looked at anaerobic prepared donor stools for transplant, and found that a third (32%) of patients achieved remission.

Positive Experiences for IBD

A website called The Power of Poop is a significant resource for FMT and tells the story of one woman’s complete recovery from an IBD, officially titled “cause unknown,” with FMT.

(I)t was my last resort, after six years of chronic pain, great expense, and a problem that was only getting worse, I felt like I had no reason not to try it. I believed it would work because antibiotics always seemed to help me (as did antimicrobial herbs, such as oregano oil), but only while I was taking them. I felt I needed to change my gut microfloral community and FMT seemed the best way to do that.

On the surface it seems like it would be a somewhat risky procedure, but the more I think about it the less risky it really seems. As long as you have a healthy donor the risk is really quite minimal.

The Power of Poop

Whether or Not FMT will Work for Your IBD or IBS

It has been clearly documented that there are very few negative effects from properly administered FMT, and zero serious effects as long as it is properly administered. That doesn’t mean it’s the miracle cure that many think it is, particularly as part of the recent trend for use against obesity. It’s important that you not charge into FMT as a cure, for both safety and financial reasons.

First of all, as suggested by The Power of Poop, rule out all other potential causes.

See a doctor, get a referral to a gastroenterologist and go through their standard screening. Depending on your conditions this is likely to include diet, fecal and breath tests, blood tests, colonoscopy, endoscopy, etc. Make sure that you are tested for auto-immune conditions as these often go hand in hand with gut conditions and will need to be addressed as part of a recovery plan.

The Power of Poop

They also recommend that you ensure your problem stems from dysbiosis. To find out, you can take a microbial diversity test that will confirm it, but it is pricey. Otherwise, a simple way to tell is if you have responded well to probiotics, antibiotics, or when you haven’t eaten, then your problem is probably related to dysbiosis. They note that if you do not respond to probiotics, it could still be related, but if you do then it is almost certain.

Remember, having an IBD makes you significantly more likely to contract a C. diff infection and more likely to have more, potentially life threatening, complications from it. So it is always worth looking into and completely safe, but there are methods to make absolutely sure that you will benefit.

Regulation of FMT

FMT is a very confusing treatment to classify and regulatory bodies have been struggling to do so for over a decade. It is widely used for treating C. diff in life threatening cases, but things get murkier for other applications and regulations have changed over the years.

The FDA considers FMT to be a biological product and an “investigative new drug,” which requires physicians to obtain an investigational new drug application (IND) to offer it. It is a drug that is not a drug and not easily classified. Many have suggested that it be regulated like a natural tissue, since it comes from the body, rather than an artificial substance. That would make regulation much easier and less stringent, allowing a natural treatment to become commonly practiced.

Likewise, Health Canada has regulated FMT as a “new biologic drug,” but limits its use outside of C. diff.

These regulations are relaxed, however, in cases where the disease is life threatening and all other options have been exhausted.

Recently, the IDSA has begun recommending FMT for C. diff and IBD. They also provide guidelines for treatment, which is a great first step towards more open and less stringent regulations.

Naturally DIY: Curing Your IBD or IBS at Home

Because of the stringent regulations, there are limited places and limited conditions where you can receive FMT treatment for IBD. However, it is permitted for doctors to act in an advisory capacity for you to do it yourself. As mentioned above, it is very important that you follow their advice to ensure a proper, and therefore safe, treatment.

If you decide to try DIY, you should find a physician to provide counseling and assistance (and again, The Power of Poop is a wonderful resource). They will carry out screenings, teach you the process, and recommend equipment for your own at home use.

Screen Your Donor, Screen Yourself

It has been solidly confirmed that FMT is absolutely safe, save for occasional minor issues such as mild fever, but only if it is conducted properly.

There is one warning about FMT that every potential practitioner needs to know. It is absolutely critical that you screen your donor with the highest scrutiny. Just like in a blood transfusion, you are moving someone else’s biological compound into your own body and their problems will come along with it.

The Power of Poop says that a donor should not:

  • Have had any antibiotic exposure in the past six months
  • Be immunocompromised
  • Have had any tattooing or body piercing in past six months
  • Have any history of drug use
  • Have any history of high-risk sexual behavior
  • Have any history of incarceration
  • Have recently traveled to endemic areas
  • Have any chronic GI disorders, such as inflammatory bowel disease

The Power of Poop

Donors should also be screened for any pathogens, such as Hepatitis A, B, and C serologies, HIV, RPR. ova and parasites, C. difficile, PCR, culture and sensitivity, and giardia antigen.

Before you begin FMT, you must also be absolutely sure that you yourself have been screened for other potential causes that could cause complications or infection from the transplant of someone else’s bacteria into your own biome.

Meta Analysis of Studies

Study nameResearchersTypeYearDiseaseConclusionNotes
Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA)IDSA and SHEA; L Clifford McDonald Dale N Gerding Stuart Johnson Johan S Bakken Karen C Carroll Susan E Coffin Erik R Dubberke Kevin W Garey Carolyn V Gould Ciaran Kelly Vivian Loo Julia Shaklee Sammons Thomas J Sandora Mark H WilcoxGuidelines2018C. diff, but has significant implications and discussion for IBDsPositiveIBD patients are more likely to contract C. dif. FMT is less effective for IBD's, but promising.
Fecal Microbiota Transplantation: A Review of Emerging Indications Beyond Relapsing Clostridium difficile Toxin ColitisWoo Jung Lee, MD, Lakshmi D. N. Lattimer, MD, Sindu Stephen, MD, Marie L. Borum, MD, and David B. Doman, MDReview2015ManyInconclusive
Systematic review: faecal microbiota transplantation in the management of inflammatory bowel disease.Anderson JL, Edney RJ, Whelan K.Systematic Review2012IBDPositiveWell-designed randomised controlled trials are required to investigate these findings.
Fecal microbiota transplantation: techniques, applications, and issues.Borody TJ, Campbell J.Systematic Review2012ManyPositive
Safety, tolerability, and clinical response after fecal transplantation in children and young adults with ulcerative colitis.Kunde S, Pham A, Bonczyk S, Crumb T, Duba M, Conrad H Jr, Cloney D, Kugathasan S.Study2103Ulcerative colitis in childrenPositiveFMT indicated efficacy in the treatment of UC.
Temporal bacterial community dynamics vary among ulcerative colitis patients after fecal microbiota transplantation.Angelberger S, Reinisch W, Makristathis A, Lichtenberger C, Dejaco C, Papay P, Novacek G, Trauner M, Loy A, Berry D.Study2013Ulcerative colitisNegative
Fecal microbiota transplantation: in perspectiveShaan Gupta, Emma Allen-Vercoe, and Elaine O. PetrofResearch2016Ulcerative colitis and C. difN/A
Fecal microbiota transplant is safe and effective for patients with ulcerative colitisWeill Cornell MedicineResearch2017Ulcerative colitisPositive"A single transplant of microbes contained in the stool of a healthy donor is a safe and effective way to increase diversity of good bacteria in the guts of patients with ulcerative colitis, according to new research. The findings suggest that fecal microbiota transplantation (FMT) might be an effective treatment for the disease, which causes inflammation and ulcers in the digestive tract."
Ongoing Clinical Trials - Crohn'sCurrentCrohn'sNA
Ongoing Clinical Trials - UCCurrentUCNA
Ongoing Clinical Trials - IBDCurrentIBD

Conclusion of Using FMT for IBD

Fecal microbiota transplant, FMT, is a completely natural process that has used natural healing products for at least 1,700 years.4 First ensure that you will benefit from it, and then it is absolutely critical that you screen your donors as well as yourself. Carrying out the process by yourself and at home is a cheaper and easier option. If you do, there are physicians that will provide counseling and you should be sure to follow their advice. If you follow these steps then FMT is an exceptionally safe treatment and is completely worth looking into.

  1. The Excrement Experiment, New Yorker (2014)
  2. See, for instance, this paper on the gut-brain axis (GBA).
  3. Costello SP, Hughes PA, Waters O, et al. Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative ColitisA Randomized Clinical TrialJAMA. 2019;321(2):156–164. doi:10.1001/jama.2018.20046
  4. Should we standardize the 1,700-year-old fecal microbiota transplantation?

Yury Tsukerman