normal flora microbiota gastrointestinal tract medicine

How fecal microbiota transplants can improve lives and possibly save them

The Wonders of Fecal Transplants

Fecal microbiota transplantation is the new ‘it’ treatment. Here’s why you should give a s**t.

When you think of futuristic medical treatment, the images that pop into your mind are probably along the lines of organs grown in a petri dish or fancy high-tech equipment. I bet you don’t think of poop being taken from one person and given to another, but that is where the future of gastrointestinal treatment (and possibly treatment of many other diseases) is headed. Fecal microbiota transplantation (FMT), also called fecal bacteriotherapy, is not a new concept. People all over the world have been using variations of it for centuries, but it’s only in recent years that modern medicine has begun to embrace it and really attempt to get to the bottom of it. Let’s try and get over the initial yuck factor and dive into why this treatment is actually quite awesome.

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Fig 1. “Stool sample” photo taken by Emily S. Melzer

Before we talk about the procedure, let’s back up and go over the term “normal flora” or “microbiota”. All animals have many microbes living in and on them, and humans are no exception. The estimate used to be that for every human cell in the body there were 10 non-self microbial cells. However, that number is most likely closer to a ratio of 1:1 [1]. Just to put this into perspective, a normal human gut has between 500-1000 different bacterial species! You may already know that most of these microorganisms mean us no harm, and in fact do us a whole lot of good. From battling harmful disease-causing microbes (pathogens) and assisting in digestion, to maintaining a healthy immune system and producing vitamins for us – these microbes are mostly friends, not foe.

The tricky part is that our body is a complex ecosystem, where there are both good and bad players and balance is everything. How many cells we have of each species is critical to an individual’s health. There are many factors that affect this balance, including diet, antibiotic treatment, genetic factors, hygiene, and certain diseases. A microbial imbalance is termed “dysbiosis” and may result in the bad bacteria winning over the good bacteria, which may cause complications such as inflammatory bowel disease, obesity, diabetes and many other disorders [2].

What can be done to get a microbial community back on track? When a patient has a dysfunctional kidney and needs a replacement, we find a kidney donor. And when a patient has a pathogenic microbial hostile takeover, we look for someone to donate… microbes. But how does one do that? As gross as it may sound, one of the most effective ways to treat a patient’s imbalanced gastrointestinal tract is with a fecal transplant. If you’re thinking ‘ew, disgusting!’ that’s ok, just keep reading.

First of all, since the risks of a transplant can be very high and pathogens might end up being transferred from the donor to the recipient, donor screening is an extremely rigorous process. Donors may be relatives, friends, or strangers. Although researchers have shown that treatment tends to be slightly more effective when the donor is a partner or a close relative who shares the same environment [2]. The general idea is that the donor’s stool is diluted with saline, mixed together and then filtered to get rid of particulates. The delivery method varies and can either be through the lower gastrointestinal tract using colonoscopy, or it could be nasogastric, which means using a tube that goes through the nose to the upper gastrointestinal tract. Alternatively, there have been attempts to deliver the microbial transplanted community in a pill that the patient can ingest [3].

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Fig. 2. Human gastrointestinal tract (Source: Wikipedia)

This sounds nuts, could it really work? Let’s look at the example of Clostridium difficile infection. Infection by this bacterium may cause inflammation of the large intestine and is potentially fatal. In 2010 C. difficile infections killed 15,000-20,000 people in the U.S. alone and infection numbers are on the rise, partly because drug resistance is becoming more prominent. While other treatments for this disease are failing, FMT has shown to be extremely effective with a cure rate of over 90%, for the most part after a single treatment [4].

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Fig. 3. Clostridium difficile spores. (Source: Wikipedia)

At the moment, the FDA regards FMT an experimental drug, and additional research is needed in order to standardize the procedure, as well as possibly expand its use to treat other disorders such as autoimmune diseases. Feces is something we don’t really like to talk about (unless you’re five years old and it’s a potty joke) but hopefully we can look past that and appreciate the power that our microbial community has on our health and how brilliant it is that we can share these communities to cure serious disease. This is the perfect example of the cheesy old saying “a candle loses nothing by lighting another candle”. Those with healthy microbiota have pretty much endless supplies of poop to donate to those in need of FMT and we should not only give a s**t but also be excited about this easy, low risk, inexpensive and effective treatment.


  1. Sender, R., Fuchs, S., & Milo, R. (2016). Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell, 164(3), 337-340.

  2. Choi, H. H. and Cho, Y. S. (2016). Fecal Microbiota Transplantation: Current Applications, Effectiveness, and Future Perspectives. Clin Endosc. DOI:

  3. Biliński J, Grzesiowski P, Muszyński J, Wróblewska M, Mądry K, Robak K, Dzieciątkowski T, Wiktor-Jedrzejczak W, Basak GW. (2016). Fecal Microbiota Transplantation Inhibits Multidrug-Resistant Gut Pathogens: Preliminary Report Performed in an Immunocompromised Host. Arch Immunol Ther Exp. DOI 10.1007/s00005-016-0387-9

  4. Bakken, J. S., Borody, T., Brandt, L. J., Brill, J. V., Demarco, D. C., Franzos, M. A., … Surawicz, C. (2011). Treating Clostridium difficile Infection with Fecal Microbiota Transplantation. Clinical Gastroenterology and Hepatology : The Official Clinical Practice Journal of the American Gastroenterological Association, 9(12), 1044–1049.

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