Faecal Microbiota Transplants: Is poop up the pipe a panacea?

Cue scenes of nature survival tv shows telling you to pee on your wounds or to drink it when stranded at sea; let’s now see where we can stick our- excuse the vernacular- the poop. It’s not bad enough that traces freely flow into our mouths whenever we’re frolicking in the warm water at the beach or communal pool, we’re now requesting it be stuck up our pipes.

There has been increasing interest in Faecal Microbiota Transplantation (FMT), warranted too; with stories making The Sydney Morning Herald[1] of patients’ mood changes, growing hair back, and losing weight, even my hand’s up to be a guinea pig! What’s the worst that could happen?

Well, infection and ultimately death.[2]

Aside from very good data for FMT efficacy in Clostridium difficile (C diff) infections,[3],[4] other colonic conditions such as Irritable Bowel Syndrome and Ulcerative Colitis (UC) trials yielded mixed results.[5],[6] This may be attributed to a whole host of reasons comprehensively outlined for UC which includes a current lack of donor-recipient compatibility profiling, standardised study protocols, and standardisation (to a pharmaceutical model) of the donated faeces.

So where are we with this in Australia? Most practitioners aren’t familiar where FMT sits in our current healthcare landscape. In short, there are a multitude of ongoing clinical trials for various ailments and medical practitioners can perform FMTs in hospital for C diff diagnosed patients.[8] Currently there is no regulated donor bank, no standardised preparation technique, no consistency in delivery methods. Since human faeces comprise of a myriad of components including food, protozoa, bacteria, archaea, fungi, viruses, and cells and secretions such as bile acids, a bespoke regulatory framework is urgently required.[9]

Sounds a bit like we’re running before we can walk, in the process soiling ourselves, or in this case- on someone else, with multiple conditions FMT alone may not remedy.

Here are a few findings that have not made the big headlines:

  • Diseased colons often have a lower diversity of bacteria[10]; studies have shown a significantly increased microbial diversity after FMT despite being therapeutically unsuccessful.5
  • An FMT preparation that was sterile-filtered for Faecal Filtrate Transfer (FFT) that contained no live bacteria, was still shown to be effective in C diff[11]
  • Some studies ‘cleanse’ the colon before FMT, and some don’t, however bowel cleansing alone can change the composition of the microbiota.[12]
  • Even placebos vary across FMT studies with water enema, isotonic saline, and autologous faecal transplant.5 Autologous transplants can affect the microbiome giving false-positive readings.[13]

In the century of quick fixes, although googling and clicking on linked stories that appear to confirm and feed our health (mis)conceptions, a whole lot of time and effort is actually required to form quality plausible evidence to support individual indications.  Faecal Microbiota Transplantations for most proposed conditions is a far cry from this endpoint, and cannot be precluded from the main message, and that is that we must be vigilant as both practitioners and patients when a poo-good-to-be-true panacea is placed before us.

Written By Lara Pham



[1] Biegler, P. (2018, March 30). Creating Crapsules: Is faeces in a pill the cure of our ills? Retrieved from The Sydney Morning Herald:

[2]Brooks, M. (2019, June 13). Fecal Transplants May Transmit Deadly Drug-Resistant Infections, FDA Warns. Retrieved from Medscape:

[3] Bakken, J. S., Borody, T., Brandt, L. J. et al. Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol, 2011 (12) 1044-1049.

[4] Van Nood E., Vrieze, A., Nieuwdorp, M. et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med, 2013 (368), 407-415.

[5] Rossen, N. G., Fuentes, S., van der Spek, M. J. et al. Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology, 2015 (149), 110-118.

[6] Halkjaer, S. I., Christensen, A. H., Lo B. Z. S. et al. Faecal microbiota transplantation alters gut microbiota in patients with irritable bowel syndrome: results from a randomised, double-blind placebo-controlled study. Gut, 2018 (67), 2107-2115.

[7] Fairhurst, N. G. & Travis, S. P. L. Why is it so difficult to evaluate faecal microbiota transplantation as a treatment for ulcerative colitis? Intest Res, 2018 (16), 209-215.

[8] (2019, September 19) TGA regulation of faecal microbiota transplant (FMT) products in Australia. Retrieved from The Department of Health Therapeutic Goods Administration:

[9] Costello, S. P. & Bryant, R. V. Faecal microbiota transplantation in Australia: bogged down in regulatory uncertainty. Internal Medicine Journal, 2019 (49), 148-151.

[10] Ott, S. J., Musfeldt, M., Wenderoth, D. F., et al. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut, 2004 (53), 685-693.

[11] Ott, S. J., Waetzig, G. H., Rehman, A. et al. Efficacy of sterile fecal filtrate transfer for treating patients with clostridium difficile infection. Gastroenterology, 2017 (152), 799-811.

[12] Jalanka, J., Salonen, A., Salojarvi, J. et al. Effects of bowel cleansing on the intestinal microbiota. Gut, 2015 (64), 1562-1568.

[13] Gough, E., Shaikh, H., & Manges, A. R. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis, 2011 (53), 994-1002.


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