19. Jun, 2019

Faecal microbiota transplantation

Faecal microbiota transplantation (FMT) comes with risks just like any other medical treatment. It can have devastating, even lethal consequences if not properly screened and administered.

Most importantly, we really only have sufficient evidence for the use of FMT in the treatment of Clostridium difficile (C.diff) infections.

All other conditions are still considered to be in the investigational stage, so it is important to be aware of the possible side effects. These can include weight gain or loss and change in mood, particularly depression. This is not surprising given what we know about the gut-brain axis, and the link between food and mood.

Although successful in approximately 80% of C.diff infections, recurrence can occur in as little as a month, so it is certainlly not a miracle cure. For successful transplants though, the improvement in quality of life is marked, even if only for a short time.

"In 2015, the Gastroenterological Society of Australia recommended that..

“FMT should be made available as a treatment option for all patients in the Australian healthcare system with recurrent or refractory [Clostridium difficile infection (CDI)]. This requires that FMT services be developed in at least one public hospital in each state or territory”and

“FMT for indications other than for CDI should be carried out only in the clinical trial setting and with careful evaluation and transparent reporting of efficacy and safety”.

If you are considering FMT, please speak to your GP first so you can make an informed decision. As it is still very much in its infancy, we have no idea what the long term consequences may be.

Given the evidence we have showing the association of certain microbiota with numerous diseases (physical and mental), I urge you to err on the side of caution. 


Gastroenterological Society of Australia 2015, GESA Position Statement on Faecal microbiota transplant (FMT)

Jackson et al. 2018, 'Gut microbiota associations with common diseases and prescription medications in a population-based cohort', Nature Communications, vol.9, no. 2655

Mcilroy et al. 2018, 'Current and future targets for faecal microbiota transplantation', Human Microbiome Journal. Vol.11

RACP 2019, Much more than a gut feeling for faecal transplant patients, <


Sparke, C 2019, Warning over safety of faecal transplants, <https://www.ausdoc.com.au/news/warning-over-safety-faecal-transplants>

Want et al. 2017, 'The Human Microbiota in Health and Disease', Engineering, vol.3, no.1, pp.71-82