The gut microbiome: what is proven – and what is just sold

Few research fields have generated as much excitement as the gut microbiome. Gut bacteria are said to shape our weight, our immunity, even our mood. That excitement has become a market: home stool tests, "personalised" bacterial capsules, gut cleanses. Yet between what research shows and what is sold lies a wide gap. This article separates the established from the promised.

What the microbiome is – and why it fascinates

The gut microbiome is the community of microorganisms living in the gut – mostly bacteria, plus viruses and fungi – together with their genes. These microbes digest what we cannot, especially fibre, producing short-chain fatty acids, and they interact constantly with the gut lining and immune system. Such a large, changeable ecosystem plausibly influences many diseases – hence the excitement.

The core problem: association is not causation

Most human microbiome findings come from cross-sectional studies comparing sick and healthy people at one point in time. Such a difference does not reveal what came first: a disease can change the microbiome (reverse causation), and diet and drugs change both at once. In a Dutch analysis of 1,883 people, 19 of 41 drug groups were associated with microbiome differences; the strongest were proton pump inhibitors (acid blockers), metformin (a diabetes drug), antibiotics and laxatives. A "typical diabetic microbiome" may largely reflect the medication.

Many striking results come from germ-free mice, whose gut and immune system differ substantially from ours. What works in a mouse is a hypothesis for humans, not proof.

Established medicine: faecal transfer for recurrent C. difficile

Clostridioides difficile is a gut bacterium that thrives after antibiotics and can cause severe, recurring diarrhoea. In a randomised trial from Amsterdam (NEJM, 2013), 13 of 16 patients (81%) were cured after a single infusion of donor stool, versus 4 of 13 (31%) on the antibiotic vancomycin alone.

Guidelines now endorse faecal microbiota transfer (FMT). The European society ESCMID (2021) prefers FMT or the antibody bezlotoxumab, added to standard antibiotics, from the second recurrence. The US societies IDSA/SHEA (2021) place FMT after multiple recurrences despite appropriate antibiotics. In the US, standardised microbiota products have been approved since 2022 (Rebyota, rectal) and 2023 (Vowst, oral capsules); in the Vowst trial, 12.4% recurred versus 39.8% on placebo. As of May 2026, Vowst is still awaiting EU approval. In Germany, donor stool counts as a medicinal product; hospitals prepare FMT individually under the treating physician's responsibility.

Conversely, antibiotics are the strongest known disruptor of gut flora. In the American Gut project, people who had taken antibiotics in the previous month had a less diverse microbiome. Using them only when needed is the best microbiome protection.

Probiotics: where the evidence is – and isn't

For probiotics – live microorganisms meant to confer a health benefit – the best evidence concerns preventing diarrhoea during antibiotic treatment in children. A Cochrane review (2019; 33 trials, 6,352 children) found a moderate reduction: nine children need to be treated for one to avoid diarrhoea. Lactobacillus rhamnosus and Saccharomyces boulardii at high doses (5–40 billion organisms a day) performed best. The American Gastroenterological Association (AGA, 2020) suggests specific strains to prevent C. difficile in adults and children on antibiotics – a conditional recommendation based on low-certainty evidence. Preventing necrotising enterocolitis, a dangerous gut inflammation in preterm infants, is a specialised neonatal-unit use.

For irritable bowel syndrome (IBS) the picture is mixed. The German S3 guideline (2021) says selected probiotics "should" be used (grade B recommendation); the AGA recommends them for IBS only within clinical trials. For healthy people and general "gut health" there is no convincing evidence.

Effects apply to the strain tested, not to "probiotics" in general. Most shop-bought capsules are food supplements, sold without approval (see our supplements evidence check). Germany's consumer advice centres (Verbraucherzentrale) note that the EU has approved no health claim for supplements with specific bacterial cultures, and that 27% of products in one official test did not contain the declared bacterial count. They advise against them for people with weakened immunity or after transplantation.

Diet: fibre, variety, fermented foods

The "30 plants a week" advice comes from the American Gut project (2018, over 11,000 participants). There, 41 people eating more than 30 plant types a week had a more diverse microbiome than 44 people eating ten or fewer. That is an observation in volunteers – not proof that 30 plants make anyone healthier.

In a small randomised Stanford trial (Cell, 2021), 36 healthy adults spent ten weeks eating either much more fibre or many fermented foods such as yoghurt, kefir and kimchi. With fermented foods, microbial diversity rose and 19 inflammatory markers fell, including interleukin-6 – but the primary outcome, an immune response score, did not change in either group. On ultra-processed food, a feeding study in 16 healthy people found that the emulsifier carboxymethylcellulose reduced microbial diversity within 11 days; whether that matters clinically is unknown.

Crucially, sound dietary advice does not depend on the microbiome. The German Nutrition Society (DGE) sets a guide value of at least 30 g of fibre a day; higher intake is linked to lower mortality and less heart disease, diabetes and colon cancer. Average intake in Germany is well below that. Whole grains, pulses, vegetables and nuts are worth it whatever microbiome research concludes.

Consumer microbiome stool tests

Commercial tests sequence bacterial DNA in stool – a single marker gene (16S) or all of it (shotgun sequencing). The US standards agency NIST sent identical portions of a reference stool to seven companies. Of 1,208 genera reported, only three appeared in every result. Differences between companies were as large as those between different people; three reported C. difficile, four did not.

There are no validated reference ranges for a "healthy" microbiome. An international consensus of 69 experts (2025) found insufficient evidence for routine testing, discouraged self-requested tests and found no agreed definition of "dysbiosis". The German IBS guideline is explicit: analysis of the normal gut flora should not be performed. The sales pattern is familiar from the longevity market.

Research, not yet practice

• Cancer immunotherapy: In melanoma resistant to immunotherapy, 3 of 10 patients responded again after stool transfer from responding donors – an uncontrolled signal, not proof.
• Colorectal cancer: E. coli strains producing the toxin colibactin leave a mutation pattern in lab-grown mini-guts that also appears in some colorectal tumours. No test follows from this; colonoscopy remains the tool (more on bowel cancer screening).
• Fatty liver (MASLD): In a small randomised trial, donor stool reduced liver fat no more than returning patients' own stool. Weight loss and exercise remain what works (more on fatty liver).

What this means for you

• Eat a fibre-rich, plant-forward diet; fermented foods are a reasonable addition.
• Take antibiotics only when needed – and then as prescribed.
• If you tend to get diarrhoea on antibiotics, ask about a tested strain at an adequate dose.
• Persistent bowel symptoms, blood in the stool or weight loss need a doctor, not an online stool test.

Questions before buying a test or probiotic

1. What decision would I make differently based on the result?
2. Has this exact strain, at this dose, been tested in randomised trials for my problem?
3. Does the test company also sell the "matching" products?
4. Do I have weakened immunity, a central venous catheter or a transplant?

This article is general information and not individual medical advice. Decisions about tests and treatment belong in a conversation with your own physician.