Could faecal transplants cause long-term health problems?
Keeping a healthy mix of friendly microbes in the gut – known as eubiosis – is crucial for good health. When that delicate balance is thrown off – often by antibiotics, diet or illness – the result can be a range of issues, from digestive problems to more serious conditions like Crohn’s disease, ulcerative colitis, and even neurological and metabolic disorders.
One increasingly popular way to try to restore gut health is through faecal microbiota transplantation. This involves taking stool from a healthy person, isolating the beneficial microbes and putting them in a capsule (jokingly referred to as “crapsules” or “poo pills”). The hope is that the beneficial microbes in the pill will establish themselves in the patient’s gut, thereby improving microbial diversity and function.
Faecal transplants have been used to treat a wide array of conditions, including irritable bowel syndrome, Parkinson’s disease, obesity and Type 2 diabetes.
Although generally viewed as safe and effective, a new international study published in the journal Cell has raised some concerns. The scientists found that when the donor’s microbes do not properly match the recipient’s gut environment – a situation they describe as a “mismatch” – the treatment can disrupt the body’s metabolic and immune systems, possibly with long-lasting consequences.
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The term “mismatch” comes from the world of organ transplants, where the recipient’s body rejects the donor organ. In this case, the problem is that microbes from the donor’s large intestine may not be suitable for other parts of the recipient’s gut, especially the small intestine, where the microbial makeup is very different.
To test this, researchers gave antibiotics to mice to disturb their natural gut microbes, then treated them with faecal transplants. They also tried transplanting microbes specifically from different parts of the small intestine. The mice were monitored for one to three months to track changes.
Wrong microbes in the wrong place
They found that faecal transplants often led to regional mismatches – the wrong microbes ending up in the wrong place. This altered the mix and behaviour of the gut microbes in unexpected ways, disrupting energy balance and other functions.
Biopsies from the gut and liver showed significant, lasting changes in how certain genes – particularly those linked to metabolism and immunity – were being expressed.
The study did not specify exactly what kind of health issues might result from these genetic shifts. But the researchers are urging doctors to take greater care when using faecal transplants, particularly when it comes to dose, timing and possible side-effects.
There may, however, be a better way forward. A newer method known as the “omni microbial approach” involves transferring microbes from all parts of the intestine, not just the colon. This could help recreate a more balanced and natural gut environment, avoiding the local mismatches seen in standard faecal transplants.
There is also growing interest in techniques that aim to “terraform” the gut: deliberately reshaping specific regions with carefully selected microbes to restore normal function.
This new research has certainly sparked debate around the safety of faecal transplants. But with alternative approaches already being developed, there is real hope that the benefits of gut-based treatments can still be delivered, without the risks.
Georgios Efthimiou does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.