The Dangers and Risks of FMT (Fecal Microbiota Transplantation)

risk of fmt

Fecal microbiota transplants (which are also known simply as fecal transplants or FMT) involve the transfer of feces from one individual to another. The aim of this medical procedure is to positively change the fecal microbiome of the recipient as a means to treat a number of gut diseases (1). There are many proven health benefits of FMT, especially as a remedy for Clostridium difficile but due to it being considered as a potential weight loss cure, many people are conducting the procedure without knowing the risks or side effects. FMT has huge potential as a miracle cure for many ailments far beyond the gut, but until the mechanism is fully understood, one must proceed with caution. To find out the risks of FMT and see if FMT is for you, then read on.

What is FMT?

FMT may appear to be a novel procedure, but the practice actually dates back to the 4th century CE.

In a paper, a Chinese physician named Ge Hong produced advised individuals suffering from severe diarrhea to consume the fresh stool produced by a healthy neighbor.

Descriptions of fecal transplant as a clinical practice was first described in English in 1958, but Western medical researchers only began studying its efficacy in treating Clostridium difficile (CDI) infections in the early 1980s, however.

Fecal transplants have proved to be an effective means of helping patients with recurrent CDI infections, where a change in gut flora (or intestinal flora) causes antibiotic-related diarrhea that can prove to be life-threatening (2).

The introduction of normal flora from a healthy individual through the transplant of donor feces is believed to re-establish the balance in the patient’s gut microbiotic flora. Fecal transplants have also been used to treat inflammatory bowel disease and insulin resistance/metabolic syndrome.

Dr. Colleen R. Kelly, a medical professor at Brown University has pointed out that fecal transplants have been beneficial for “a lot of people who have run out of other options” (3). However, she warns that “there is a lot we don’t know in terms of side effects/risks and long-term safety.”

Doctors and medical researchers are still studying the complex relationship between gut flora and human health (especially over a long-term period) to safely manipulate gut microbiota, but here are some of the fecal transplant risks that are currently known.

Check them out.

risks of FMTThe risks of FMT

  1. Obesity

One of the greatest health benefits of FMT is also one of the biggest risks of FMT. This is weight gain or weight loss. It is a significant side effect.

An influential 2015 journal article published in Open Forum Infectious Diseases and established that fecal transplants can result in the onset of obesity in the receiver (4).

In one instance, the donor (the patient’s daughter) was a healthy but overweight woman. The recipients suffered from no further CDI recurrence after the procedure but had become obese when she reported back to the hospital 16 months later.

Her BMI had increased from 26 to 33, and her weight had increased from 136 pounds to 170 pounds. Despite undergoing a diet and exercise program, she continued to gain weight. In another 20 months, her weight increased to 177 pounds, and she exhibited constipation and “unexplained dyspeptic symptoms”.

The publication of this article led to the introduction of a policy to only use non-obese donors for FMT and a growing body of research on the interconnections between an individual’s body mass index (BMI), metabolism, and gut microbiota.

Researchers, as you can imagine, are looking very closely into FMT as a weight treatment program by using the gut bacteria of slim donors to treat obesity. The link between gut bacteria and weightloss (or indeed, weight gain if the donor is obese) has only just begun.

  1. Flares of underlying inflammatory bowel disease

One of the most common risks of FMT is potential complications for people with chronic bowel problems.

A 2013 journal article published in Clinical Gastroenterology and Hepatology reported that the use of fecal transplants for CDI can result in flares of underlying inflammatory bowel disease (5). This offers contradictory evidence to the 91% success rate in using fecal transplants to treat CDI without significant reported complications.

In this instance, a 78-year old male patient with ulcerative colitis (an inflammatory bowel disease which results in long-term inflammation and ulcers in the digestive tract) that had been quiescent for over two decades was treated with a fecal transplant after experiencing 3 episodes of CDI.

The donor stool was provided by his wife, who had presented no comorbidities and no recent antibiotic use during the screening process. She had also tested negative for STIs and other transmissible pathogens.

Nine days after the procedure, the patient began exhibiting symptoms which were consistent with what he had experienced during previous CDI infections. His ulcerative colitis (UC) condition was also exacerbated.

The researchers theorized that the introduction of the new microbiota may have an immune response or a change in mucosal integrity or perhaps the introduction of an unwanted pathogen (6).

Patients who suffer from IBD flare usually have low immunity levels (children, senior citizens, and individuals with immune disorders) and should be administered with FMT through a lower gastrointestinal route.

  1. Side effects of FMT administration

The administration of the procedure is always a common risk of FMT.

An FMT can be administered via upper or lower gastrointestinal routes. The former includes administration by capsule, or via tube,  direct into the stomach or intestines.  The latter consists of administration via colonoscopy or retention enema after the patient has undertaken bowel lavage and/or antibiotics (7).

Lower gastrointestinal routes were found to be more widely used, and presented a lower risk of adverse effects. On the other hand, upper gastrointestinal routes were associated with side effects such as nasal stuffiness, sore throat, rhinorrhea and upper gastrointestinal hemorrhage (8).

It was theorized that this occurred due to injury when invasive endoscope procedures were used to deliver the donor fecal transplant.

While abdominal comfort occurred more commonly in patients who experienced administration via the upper gastrointestinal route, several symptoms were common to both modes. These included abdominal pain, flatulence, bloating, cramps, a transient fever and increased stool frequency.

  1. Death

A systematic review of the adverse events following FMT published in Public Library of Science one listed death alongside pathogen infections, IBD flares, auto-immune diseases and injuries sustained during the FMT procedure as severe adverse events that were attributable to FMT.

Death occurred in 38 separate patients, and was recorded in 10 different publications. The mortality rate was 3.5% (38/1089) (9).

However, 35 out of these 38 death incidents were not related to FMT and were instead caused by the patient’s underlying conditions.

Out of the three deaths that were related to FMT, one was caused by “aspiration during sedation of colonoscopy”. The other two were caused by infections that may have resulted from the FMT procedure or a pre-existing immune disease.

  1. Infection

Despite stringent screening procedures to ensure that FMT donors are healthy, recipients still bear some risk of being infected by the donor stool sample.

In the previously mentioned 2016 systematic review, twenty-seven patients were found to have been hospitalized or died from a severe infection. The incidence of severe infection was thus 2.5% (27/1089) (10).

Out of these 27 cases, 8 were found to be related to FMT.

Two were caused by a viral infection (cytomegalovirus and norovirus), two more were caused by a bacteremia infection (Escherichia coli, Proteus mirabilis, Citrobacter koseri, and Enterococcus faecium) and the remaining four were due to infection by unknown pathogens.

The cytomegalovirus infection occurred during a home FMT and is believed to have been caused by the use of stool from a child donor who had not been properly screened.

Meanwhile, the norovirus infection was believed to have been caused by environmental contamination by an endoscopy suite employee.


As more data and research is conducted, the risks of FMT procedure for the patient is likely to decrease. The physical injuries sustained from the administration process can be avoided by high standards of care, and by opting for non-invasive administration via the lower gastrointestinal routes.

Meanwhile, the risk of transferring viruses, bacteria, pathogens, or harmful gut flora from the donor to the patient can be reduced by stringent and thorough donor screening.

Many patients express a preference for family members as donors. This is not necessarily an issue if the family member in question is of optimal health.

However, screening and testing is not optional even in this case, as he or she may be asymptomatic for STDs, pathogens, or other transferable diseases.

Finally, patients with a history of bacteremia, inflammatory bowel disease, and immune diseases should proceed with extreme caution.

Rigorous testing of potential donors will reduce the risks of FMT associated with poor quality donors but it cannot eliminate them altogether.

The relationship between gut flora, epigenetics, and the immune system is not fully understood at this point. Doctors may thus fail to foresee how healthy gut flora in the donor can result in a harmful immune or genetic reaction in the recipient.

Doctors may thus fail to foresee how healthy gut flora in the donor can result in a harmful immune or genetic reaction in the recipient.

There is nevertheless reason for optimism. The Human Microbiome Project (HMP) has discovered that the microbiome is more varied than the human genome and easier to modify, after sampling the microbiome of numerous individuals.

When this variability in donor microbiota is better understood, better metagenomics, genetic and microbiota donor screening methodologies can be formulated (11).

Soon the risks of FMT will fall, and the benefits will be widespread.


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