Health Articles

Poop as Medicine – What is FMT?

FMT stands for Fecal Microbiota Transplant, which is ‘the process of restoring the bacteria commonly found in a healthy human gut’ (according to the Taymount clinic).

Or, to put it in plain English: implanting a healthy person’s stool (+ microbiome) into a sick person’s gut.

The reason I wanted to share this information is that I’ve had FMT myself and will be sharing my experience in the future.

Although the idea of stool transplants been around for a long time (there’s evidence of similar procedures in ancient China [1]) and the procedure can even be observed in nature (for example animals eating faeces [2]) it has only recently been implemented in a clinical context and has emerged as potentially the most effective treatment for recurrent C. Difficile infections [3] (an antibiotic-resistant bacterial infection that can lead to severe diarrhoea, sometimes with fatal outcomes).

The Idea behind FMT

In recent years, more and more science has been emerging on the importance of the gut microbiome for human health.

Likewise, a change in the balance of the gut microbiome has been linked to chronic disease.

Supplements of different strains of beneficial bacteria (probiotics) are available but we know that the gut microbiome is so much more complex than just a few strains – plus, there is still a lot we don’t know.

In light of these shortcomings, the idea behind FMT is to transplant a microbiome in its whole complexity into a sick person’s gut so that it may be restored.

How It Works

Basically it works by taking the stool of a healthy person and ‘infusing’ it into the colon of a sick person.

Some desperate people have gone down the DIY path – this usually involves stool, a blender, saline solution and an enema bag. Sounds messy and sure comes with many risks.

In a clinical context the donors are carefully selected and screened for all sorts of diseases plus their physical fitness, mental state, medication history and BMI.

Because many of the microbes in our gut are anaerobes, an anaerobic environment is maintained when collecting and preparing the transplants. Any waste material is then filtered so that the Fecal Microbiota Transplant mainly contains the microbes.

The transplant is usually administered by colonoscopy, endoscopy, sigmoidoscopy or enema. ‘Poop pills’ are also being developed to make the procedure easier and more accessible.

As a preparation, the colon is usually ‘cleaned’ by use of laxatives and colonic irrigation.

In most cases, 5 – 10 implants are used, sometimes more and over a longer period.

What Conditions Is FMT Used For

So far, C. Difficile is the main condition that FMT is an accepted treatment for.

However, FMT has been used by people with a range of conditions that have one thing in common: an altered gut flora.

Examples are:

  • Inflammatory Bowel Diseases (Crohn’s Disease & Ulcerative Colitis)
  • Constipation
  • Chronic Diarrhoea
  • Irritable Bowel Syndrome – IBS (Post-Infectious, Post-Antibiotic)
  • Obesity
  • Neurological conditions such as:
    • ME (Myalgic Encephalopathy)
    • CFS (Chronic Fatigue Syndrome)
    • MS (Multiple Sclerosis)
    • Parkinson’s Disease

Does this mean it’s effective for all these conditions? No – more research needs to be done and from what I’ve heard the outcomes can be very individual.

Interstitial Cystitis and FMT

There is a link between IC, an altered bladder microbiota and an altered gut flora.

Theoretically, modulating the gut flora may be beneficial.

However, there is absolutely no evidence supporting the use of FMT for IC.

Have you received FMT, or are you thinking about it? What are your thoughts? Let me know in the comments!

Pin it for later:


  1. van Nood, Els et al Fecal microbiota transplantation: facts and controversies Current Opinion in Gastroenterology: January 2014 – Volume 30 – Issue 1 – p 34–39
  2. National Geographic Why Do Animals – Including Your Dog – Eat Poop? May 2015
  3. Nice Faecal Microbiota Transplant For Recurrent C. Difficile Infections March 2014



  • Reply


    January 8, 2018

    I’ve always been curious about this and would like to try at some point if possible!

  • Reply


    May 6, 2018

    Thanks for sharing! I’ve had a history of IBS, gut parasites, and UTIs, and I’ve just started FMT. Have you noticed any difference with your urinary tract health since starting FMT at all?

    • Reply


      May 7, 2018

      I had the FMT after my chronic bladder issues had already disappeared so I can’t say, sorry!

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