The gut microbiome: what we know and what we don't
The trillions of microbes living in the gut are one of the most active areas of health research. That makes it an exciting subject, and also one where marketing often runs ahead of the evidence.
Gut health
What the microbiome is
"Gut microbiome" describes the bacteria, fungi, viruses and other microbes that live in the digestive tract, mostly in the large bowel, together with their genes. Each person's microbiome is different, and it changes with diet, medicines (especially antibiotics), age, illness and where we live.
What we know
What we know- Gut microbes help to break down fibre that our own digestive enzymes cannot, producing substances the body uses.
- Diet shapes the microbiome. A varied diet that is high in fibre from plants is consistently linked with a more diverse microbiome.
- Antibiotics can disturb the microbiome, which is one reason they should be used only when needed.
What is promising but not settled
What may helpDifferences in the microbiome have been linked with conditions including irritable bowel syndrome (IBS), obesity, type 2 diabetes and inflammatory bowel disease. Most of this research shows associations. In most cases it has not yet shown that changing a person's microbiome prevents or treats these conditions.
Probiotics may ease some symptoms of IBS for some people, but the NHS notes there is little evidence for many of the health claims made about them. Probiotics are generally sold as food supplements, not medicines, so they are not tested in the same way. NICE advises that people with IBS who choose to try one should take it for at least four weeks while monitoring the effect.
What we don't yet know
What we don't yet knowThere is no agreed definition of a "healthy" microbiome for an individual. An international consensus of 69 experts, published in 2025, concluded that there is insufficient evidence to recommend the routine use of microbiome testing in clinical practice. It advised that any test should be requested by a qualified healthcare professional, interpreted alongside the person's history, medicines and symptoms, and not used on its own to decide treatment.
A stool microbiome test describes which microbes were present in one sample. On its own it cannot diagnose the cause of digestive symptoms, and it does not replace the tests used in UK guidance to investigate them.
Practical steps with good support
- Aim for the NHS recommendation of 30g of fibre a day from a variety of plant foods, increasing gradually.
- Take antibiotics only when prescribed and exactly as directed.
- If you have persistent digestive symptoms, get them assessed rather than relying on a home test. Read when digestive symptoms need checking.
References
- Porcari S, et al. International consensus statement on microbiome testing in clinical practice. The Lancet Gastroenterology & Hepatology, 2025; 10(2): 154–167.
- NHS. Probiotics. Accessed 29 September 2026.
- National Institute for Health and Care Excellence. Irritable bowel syndrome in adults: diagnosis and management (CG61).
- NHS. How to get more fibre into your diet. Accessed 29 September 2026.
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