"All disease begins in the gut." — Hippocrites
What is a Faecal Transplant?
It's more than someone's poo. It could be life changing.
The Process
Faecal Microbial Transplant (FMT) begins with carefully selecting and screening a donor to ensure the stool is free from infections and other risks. The healthy donor material is then processed into a safe form — either as capsules or via a colonoscopy delivery. The procedure is performed in a clinical setting by a gastroenterologist, following strict safety and regulatory guidelines.
The Science
The human gut contains trillions of bacteria that play a critical role in digestion, immunity, and even mood regulation. When this delicate balance is disrupted — often by antibiotics, illness, or diet — harmful bacteria can take over. FMT works by introducing a complete, healthy microbiome from the donor into the patient, helping to restore normal microbial diversity and function. Research shows that this can help re-establish healthy gut ecosystems and improve related symptoms.
The Benefits
FMTs foster a healthy microbiome more effectively than antibiotics, probiotics or nutrition alone. By targeting the root cause of your symptoms — an imbalanced microbiome — FMTs give you the best chance of achieving total symptom remission. Once delivered, the host ideally adopts the microbiome profile of the donor and therefore experiences a far greater likelihood of symptom relapse.
Dive Deeper into the Science
Listen to TGA-accredited FMT provider Dr. Paul Froomes speak about the evidence and use cases for FMTs.
Want to speak to an expert?
Get in contact to find out how FMTs could help you.
The History
Faecal transplants may sound like cutting-edge medicine, but their story begins over a thousand years ago in ancient remedies — now refined into a modern, regulated treatment used to tackle some of today’s most stubborn conditions.
4th Century CE (China)
Ancient Chinese medicine describes using “yellow soup” (stool suspended in liquid) to treat severe diarrhoea.
1958 (Denver, USA)
First documented modern FMT performed to treat life-threatening Clostridium difficile infection.
2015 (Netherlands)
Development of the “Amsterdam Protocol” — standardised guidelines for donor screening and stool preparation.
2021 (Australia)
The Therapeutic Goods Administration (TGA) introduces TGO 105, a regulatory framework for the manufacture and supply of FMT products.
Who's eligible for FMTs in Australia?
Not everyone can receive FMTs — Some of the means by which you can receive FMT treatment are below.
TGA SAS
Under the TGA’s Special Access Scheme, FMT may be considered for patients with conditions where promising research exists. Access is case-by-case, requiring a medical assessment and formal application to the TGA to ensure it is clinically justified and performed under strict safety protocols.
• Crohn's disease
• Ulcerative colitis
• Irritable Bowel Syndrome (IBS)
• Autism Spectrum Disorder (ASD)
• CFS/ME
• Depression
• Bipolar Disorder
• Multiple Sclerosis
• Parkinson's Disease Non-alcoholic Fatty • Liver Disease (NAFLD)
• Metabolic Syndrome / Obesity
• Psoriasis and other inflammatory skin conditions
Clostridium difficile
For adults suffering from recurrent C. diff infection that has not responded to standard antibiotic therapy, FMT is an approved and highly effective treatment in Australia. It is supported by strong clinical evidence, with cure rates significantly higher than antibiotics alone. In eligible cases, oral capsule delivery of FMT for C. diff can attract a Medicare rebate, making it more accessible to patients.
Clinical Trials
Patients may also access FMT by enrolling in approved clinical trials investigating its use for various conditions.
Who's can administer FMTs?
There are strict legal requirements for the administration of FMTs in Australia — only TGA-accredited Gastroenterologists can manufacture and administer FMTs.
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Donors must be thoroughly screened and monitored for over 30 pathogens
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Products must meet manufacturing and safety standards (e.g., TGO 105)
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Administration must involve Gastroenterologists who have been specifically accredited by the TGA that are allowed to manufacture and administer FMT in Australia
Conditions Faecal Transplants have been studied in
Many conditions have been studied around the world for the effect of faecal transplants on symptom relief and remission. While Clostridium difficile is the most commonly treated, other conditions that have been studied can be treated in Australia under the care of a registered Gastroenterologist.
Inflammatory Bowel Disease (IBD) — Ulcerative Colitis
Paramsothy, S., et al. (2017). Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial. Lancet
Irritable Bowel Syndrome (IBS)
El-Salhy, M., et al. (2020). Efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome in a randomized, double-blind, placebo-controlled study. Gut
Autism Spectrum Disorder (ASD)
Kang, D.W., et al. (2017). Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome
Chronic Fatigue Syndrome
Borody, T.J., et al. (2019). Fecal microbiota transplantation (FMT) in chronic fatigue syndrome (CFS): a retrospective review of 60 patients. Journal of Translational Medicine
Depression
Zheng, P., et al. (2016). Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism. Molecular Psychiatry
Bipolar Disorder
Evrensel, A., et al. (2020). Fecal microbiota transplantation in the treatment of bipolar disorder: a case report. Clinical Psychopharmacology and Neuroscience
Recurrent
Clostridium difficile infection (rCDI)
van Nood, E., et al. (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. New England Journal of Medicine
Inflammatory Bowel Disease (IBD) — Ulcerative Colitis
Cui, B., et al. (2015). Fecal microbiota transplantation through mid-gut for refractory Crohn’s disease: safety, feasibility, and efficacy trial results. Journal of Gastroenterology and Hepatology
Risks of DIY Faecal Transplants
While FMT has shown promise in treating conditions like recurrent Clostridioides difficile (C. diff) infections under controlled medical settings, attempting it as a do-it-yourself (DIY) procedure at home is extremely hazardous and strongly discouraged. DIY FMT often relies on unscreened donors (e.g., family members or online sources), improvised preparation methods, and non-sterile administration, which amplify risks far beyond those in regulated clinical environments.
Disclaimer: DIY Faecal Transplants are illegal in Australia.
Unscreened donor stool can harbor harmful bacteria, viruses, parasites, or fungi. Common threats include drug-resistant bacteria (e.g., extended-spectrum beta-lactamase [ESBL]-producing E. coli or Shiga toxin-producing E. coli [STEC]), viruses like HIV, hepatitis B/C, norovirus, or parasites such as Giardia. In DIY scenarios, without laboratory testing, these can lead to severe infections, sepsis, or organ failure. Reports highlight that even seemingly healthy donors may carry asymptomatic infections, turning DIY FMT into a "game of Russian roulette."
DIY FMT heightens the risk of introducing antibiotic-resistant organisms, which are difficult to treat and can cause life-threatening bacteremia (bloodstream infections). This is particularly dangerous for immunocompromised individuals, where infections can rapidly progress to septic shock.
FMT can alter immune system activity, which in rare cases may provoke unexpected immune responses or trigger inflammation. Allergic-type reactions are uncommon but possible.
Altering the gut microbiome unpredictably may trigger autoimmune reactions, exacerbate conditions like inflammatory bowel disease (IBD), or contribute to metabolic disorders. Surveys indicate DIY FMT is often tried for unproven uses (e.g., IBD or autism), with no oversight on efficacy or safety.
Unlike FDA-approved FMT products (e.g., for C. diff), DIY versions bypass donor screening protocols, increasing contamination risks. The FDA has issued multiple safety alerts on FMT-related adverse events, underscoring the need for rigorous testing.
Documented Fatal Cases from Unscreened Donors
Two notable incidents highlight the lethal dangers of inadequate donor screening, even in clinical trials—risks that are exponentially higher in DIY settings.
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2019 ESBL-Producing E. coli Incident: In a clinical trial, two immunocompromised patients developed bacteremia after receiving FMT from the same donor whose stool was not screened for ESBL-producing E. coli. One patient, a 73-year-old man with a blood disorder, died from the infection. This case, detailed in a New England Journal of Medicine (NEJM) correspondence, emphasized the need for enhanced donor screening to include multidrug-resistant organisms.
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2020 STEC/EPEC Incident: Six patients in a clinical study developed infections (four with STEC and two with enteropathogenic E. coli [EPEC]) after FMT from a donor colonized with these pathogens, which were not detected in initial screening. Two patients died following receipt of the contaminated product. This was reported in a 2021 paper in Clinical Infectious Diseases, which described adverse events in seven total recipients and recommended expanded stool testing for enteropathogens to prevent transmission.
These cases underscore that unscreened or inadequately screened donors can transmit fatal infections, a risk amplified in DIY FMT where no testing occurs. If considering FMT, consult a gastroenterologist for safe, regulated options.
A recent story in Australia
An Australian woman shares her journey of overcoming years of debilitating illness through faecal microbiota transplantation, highlighting its life-changing potential.
Want to speak to an expert?
Get in contact to find out how FMTs could help you.