Fecal transplant



Within one linear centimeter of  your lower colon there lives and works more bacteria (about 100 billion) than all humans who have ever been born. Yet many people continue to assert that it is we who are in charge of the world.

Neil deGrasse Tyson


The Birth of Poop

Newborns are born with meconium in their gut, which was, until recently, thought to be sterile.  In fact meconium is populated  with Ecoli and Lactobacillus, thought to be from the mothers digestive system. As the infant moves through the birth canal their mouth fills with bacteria further colonising their digestive system. The kissing and cuddling which babies invite continues the colonisation process and nutrients in the mother’s breast milk help grow the new bacteria.

Studies have shown that the intestinal flora of caesarean delivered and bottle fed infants takes much longer to colonise. By the time your microbiome is established it contains a zoo of bacteria all working as a key digestive organ to keep you healthy. Some practitioners speculate that health and psychological problems run in families not for genetic or social reasons, but because the causative bacteria are spread through families.

Maligned & Misunderstood

As children we grow up believing that poop is bad; that it’s a nasty, embarrassing by-product of our food. It smells foul so we shun it and call it ‘waste’. Poop and fart jokes are the mainstay of schoolyard humour and generate a ready snigger among adults. We are warned from a young age that poop is full of germs that apparently have no function other than to contaminate areas where they aren’t allowed and make us sick. However this is not the full story.

The truth is that we rely on poop for much more than digestion of our food. Healthy poop is as essential as blood and bone marrow to good health. There are over 500 bacteria and 30,000 subspecies growing in our gut contributing in different ways to our health, including our mental health. Amazingly the gut produces every class of neurotransmitter that is found in the brain including 95% of the body’s serotonin. Not only does serotonin control mood, but many other bodily functions including the movement of food through the gut.

All living creatures including human beings rely on a microbiome, a community of ‘good’ bacteria living in harmony with us keeping us healthy.  These bacteria live on the skin, mucus membranes and in the gut. When the intestinal microbiome becomes unbalanced through anti-biotics or illness it is called intestinal dysbiosis . Dysbiosis can lead to debilitating physical and mental symptoms and a vicious cycle of ill health perpetuated by inflammation, malnutrition and the development of auto-immune conditions. The exact nature of the illness will depend on the predisposition, lifestyle and genetics of the individual.


Fecal Microbiota Transplant

Fecal Microbiota Transplant (FMT) is also known as a stool transplant, bacteriotherapy and human probiotic infusion.   It is a natural, medication free way to repopulate the intestinal microbiome.  FMT involves transferring fecal bacteria  from a healthy donor to repopulate the unbalanced gut bacteria of a sick person. It is used to treat  Clostridium Difficile  (C. Diff.)  infection and increasingly other conditions such as Ulcerative Colitis, Crohns Disease and digestive illness of indeterminate cause. There is also anecdotal evidence from Professor Thomas Borody’s Centre for Digestive Diseases to suggest that FMT could benefit other conditions including autoimmune disorders, neurological conditions, obesity, metabolic syndrome, diabetes and Parkinson’s disease.  The first reported FMT was in 1958 and involved the successful treatment of four patients with pseudomembranous colitis before C. Diff. was the known cause.

FMT involves a series of infusions of stool blended with saline or distilled water. Frozen stool can also be used but takes longer to populate. Medical transfer of stool is undertaken via enema, colonoscope or nasogastric tube. Home infusion usually takes place via enema, syringe or capsule. Various parties are researching the commercial production of freeze-dried stool capsules and artificial intestinal flora.

All medical interventions come with risk. However in over 370 published reports there has been no reported infection transmitted by FMT so the risks are minimal.   A study published in the New England Medical Journal in January 2013 reported a 94% cure rate of pseudomembranous colitis caused by C Diff from FMT compared to a mere 31% with vancomycin. The study was stopped prematurely as it was considered unethical not to offer the FMT to all participants.

A 2009 study found that FMT is not only an effective and simple procedure but is more cost-effective than continued antibiotic administration and reduces the incidence of antibiotic resistance.


Donors do not have to be family members but must be tested for a wide array of bacterial and parasitic infections, be free of health problems and lead a healthy lifestyle.  As it is not easy to find a suitable and willing donor, some clinics offer donor banks to provide the comfort and convenience of regular tested donors.

donor exclusion criteria

Emerging Applications

The intestinal microbiota has been linked to a number of diseases.  The Possibilities of FMT  are best summed up by FMT Pioneers Professor Thomas Borody and Associate Professor Alex Khoruts:

“Fecal microbiota transplantation (FMT) has been utilized sporadically for over 50 years. In the past few years, Clostridium difficile infection (CDI) epidemics in the USA and Europe have resulted in the increased use of FMT, given its high efficacy in eradicating CDI and associated symptoms. As more patients request treatment and more clinics incorporate FMT into their treatment repertoire, reports of applications outside of CDI are emerging, paving the way for the use of FMT in several idiopathic conditions. Interest in this therapy has largely been driven by new research into the gut microbiota, which is now beginning to be appreciated as a microbial human organ with important roles in immunity and energy metabolism.”

“This new paradigm raises the possibility that many diseases result, at least partially, from microbiota-related dysfunction. This understanding invites the investigation of FMT for several disorders, including IBD, IBS, the metabolic syndrome, neurodevelopmental disorders, autoimmune diseases and allergic diseases, among others. The field of microbiota-related disorders is currently in its infancy; it certainly is an exciting time in the burgeoning science of FMT and we expect to see new and previously unexpected applications in the near future. Well-designed and well-executed randomized trials are now needed to further define these microbiota-related conditions.”



For more information on FMT please see the Research page. 

Fecal transplant: A safe and sustainable clinical therapy for restoring intestinal microbial balance in human disease?


Images used with thanks:

The Functions of Gut Bacteria

Types of Bacteria

Donor Exclusion Criteria

Link between microbiota and diseases outside of the gastrointestinal tract


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