Faecal microbiota transplantation (FMT), a rising method for restoring gut health, may carry unexpected risks if not carefully matched to the recipient’s needs, according to a new international study published in Cell. The research shows that when microbes from a donor do not align with the recipient’s gut environment, they can disturb metabolism and immune function, potentially with long-term effects.
Maintaining a healthy balance of gut microbes—known as eubiosis—is essential for overall well-being. This balance can be upset by antibiotics, illness, or poor diet, often leading to digestive issues and even more serious conditions like Crohn’s disease, ulcerative colitis, and neurological or metabolic disorders.
FMT involves taking stool from a healthy donor, isolating the beneficial microbes, and placing them into a capsule—sometimes jokingly called a “crapsule” or “poo pill.” The goal is to help those microbes settle in the patient’s gut and restore microbial diversity and function.
The method has been used to treat several conditions, including irritable bowel syndrome, Parkinson’s disease, obesity, and Type 2 diabetes. It is generally seen as safe and effective. However, the new study highlights that not all transplants work equally well for everyone.
Researchers used mice to test the effects of FMT after disturbing their natural gut bacteria with antibiotics. In some cases, they also transplanted microbes from specific regions of the small intestine. The mice were observed for one to three months. The study revealed that faecal transplants often caused microbes to end up in the wrong parts of the gut. This “mismatch” disrupted the gut’s microbial balance and affected how certain genes linked to metabolism and immunity were expressed, especially in the gut and liver.
Although the exact health outcomes of these gene changes are still unclear, scientists caution that mismatches could carry risks. They advise medical professionals to consider factors like dose, timing, and potential side effects more carefully when using FMT.
To reduce the chance of mismatches, a newer method called the “omni microbial approach” is being explored. It involves transferring microbes from various parts of the intestine, not just the colon. This may better recreate the natural environment of the gut. Other approaches aim to “terraform” specific regions of the intestine by using carefully chosen microbes to restore normal function.
While the new findings raise important questions about the safety of faecal transplants, researchers remain optimistic. With new techniques already in development, it may still be possible to offer the benefits of gut-based treatments without the added risk.
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