What is the Microbiome?

The human microbiome is a vast community of microorganisms—primarily bacteria—that live in and on our bodies, with the greatest concentration found in the gut. These microbes play a vital role in digestion, immune function, and even mental health. A balanced microbiome is essential for overall wellbeing, while disruptions (known as dysbiosis) have been linked to a range of medical conditions.

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What is FMT?

Faecal Microbiota Transplantation (FMT) is a medical procedure that involves transferring stool from a healthy donor into the gastrointestinal tract of a patient. The aim is to restore a healthy balance of gut bacteria, especially in individuals whose microbiome has been significantly disrupted.

 

FMT is a well-established treatment for recurrent Clostridium difficile infection and is increasingly used in ulcerative colitis. For these conditions, strong clinical evidence supports its effectiveness.

For other medical conditions—particularly those outside the gastrointestinal tract—the evidence is still emerging. Much of the interest is based on anecdotal reports and small case series rather than large, rigorous clinical trials. Outcomes may vary, and expectations should be tempered accordingly.

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How is FMT Given?

FMT can be delivered in several ways, depending on the condition and patient needs. The most common method in my practice is colonoscopy, which allows direct placement of donor microbiota into the colon.

Colonoscopy-derived FMT is performed under sedation in a hospital or day surgery setting. It enables precise delivery and visual assessment of the colon, with most patients recovering quickly and comfortably.

 

When is FMT Appropriate?

I offer FMT only as a complementary therapy, not a standalone treatment. To ensure appropriate care, I require:

• A letter explaining your background, goals, and understanding

• A letter of support from your GP

• A letter from your treating specialist confirming support for FMT

This ensures FMT is integrated into your broader treatment plan with alignment across your care team.

 

What Are the Potential Side Effects of FMT?

FMT is generally well tolerated, but potential risks include:

• Temporary gastrointestinal symptoms (bloating, diarrhoea, cramping)

• Infection transmission (minimised through rigorous donor screening; risk comparable to blood transfusion)

• Rare metabolic or neurological effects

• Risks related to colonoscopy (e.g., perforation, anaesthesia)

Importantly, the long-term effects of transferring a microbiome from one person to another are still not fully understood. While FMT can restore balance in the short term, research is ongoing into its broader implications.

 

Where is the FMT Sourced From?

I source all FMT material from BiomeBank, a TGA-approved stool bank. BiomeBank ensures the highest standards of safety, donor screening, and quality control.

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What is the Cost of Treatment?

FMT is not covered by Medicare or private health insurance, so out-of-pocket costs apply.

A detailed cost breakdown is available upon request.

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What Happens After FMT?

Post-FMT care focuses on maintaining the positive changes to your gut microbiome. I recommend:

• A combination of prebiotics to nourish beneficial bacteria

• A diverse, plant-rich diet

• Regular physical activity

• Avoiding unnecessary antibiotics

These steps help support the transplanted microbiota and promote long-term gut health.

 

Contributing to Research

We invite patients to consider enrolling in our research studies, which aim to:

• Collect and analyse microbiome samples before and after treatment

• Track clinical outcomes over time

• Evaluate FMT’s safety and effectiveness in novel indications

Participation is voluntary and does not affect access to treatment. Your involvement helps build a stronger evidence base for future care.