Gut microbiome diversity: why it matters and how to build it
A diverse gut microbiome means a community of microbes that is both rich (many different species) and even (no single species dominates). Higher diversity is repeatedly linked with better health markers in large population studies, but that link is an association, not proof that diversity itself causes health. The single change with the strongest evidence behind it is eating a wide variety of plants and fibres, with fermented foods as a promising add-on. At-home microbiome tests and most probiotic claims, by contrast, are far weaker than their marketing suggests.
Key facts
- In the American Gut Project (over 10,000 samples), people eating more than 30 plant types a week had more diverse microbiomes than those eating 10 or fewer.1
- Stanford's 2021 fermented-foods trial (36 adults, 10 weeks) found fermented foods raised diversity and lowered 19 inflammatory proteins; a high-fibre arm did neither over the same period.2
- Microbes ferment fibre into short-chain fatty acids such as butyrate, which feed the gut lining and help regulate inflammation.3
- One emulsifier (carboxymethylcellulose) reduced microbial richness in a tightly controlled human feeding trial.4
- Sending the same stool sample to seven different test companies produced dramatically different results: these tests are not clinically validated.5
What "diversity" actually means
When researchers talk about gut microbiome diversity, they usually mean two things at once. Richness is simply the count of different species or strains present. Evenness describes how balanced their numbers are: a gut where a few hundred species each hold a modest share is more even than one where a single species makes up most of the population. Ecologists combine the two into "alpha diversity" indices (such as the Shannon index) that reward both having many members and having no single member dominate.
This matters because the gut behaves like an ecosystem, not a list of ingredients. A varied, balanced community tends to be more resilient: if one group is knocked back, by a stomach bug or a course of antibiotics, others can fill the gap and keep performing useful jobs such as fermenting fibre, training the immune system, and crowding out pathogens. A community dominated by one or two species has fewer reserves to draw on. That ecological logic is the real reason diversity is treated as a rough proxy for a healthy gut, rather than any single "good bug" you can name.
Why diversity is linked to health (and the catch)
Across large studies, higher gut diversity travels with better health markers. Lower diversity has been reported in conditions including obesity, type 2 diabetes, inflammatory bowel disease and some autoimmune conditions, as summarised in a widely cited 2018 BMJ review by Valdes, Walter, Segal and Spector.6 The ZOE PREDICT 1 study, published in Nature Medicine in 2021 by Asnicar, Berry, Segata, Spector and colleagues, sequenced the microbiomes of 1,098 people and found the makeup of the microbiome was more strongly associated with cardiometabolic blood markers than genetics was, with specific species tracking favourable post-meal blood sugar and blood fats.7
Here is the catch, and it is a big one. Almost all of this is observational. Diverse microbiomes tend to belong to people who also eat more plants, drink less alcohol, take fewer unnecessary antibiotics and are in better general health, so it is genuinely hard to separate the bug community from the lifestyle that built it. Diversity may be a marker of a good diet rather than an independent cause of health. It is also not a goal in itself: diversity can include unhelpful microbes, and there is no single "correct" number to chase.
Where the evidence is only observational. The links between higher diversity and lower rates of obesity, diabetes and inflammatory disease come almost entirely from cross-sectional and cohort studies. They show association, not causation. We do not yet have large trials proving that raising an individual's diversity score, by itself, improves long-term health outcomes.
The "30 plants a week" idea and the fibre evidence
The popular "30 plant points a week" target comes from the American Gut Project, a citizen-science study led by Daniel McDonald, Rob Knight and colleagues, published in mSystems in 2018. Among thousands of participants, those who reported eating more than 30 different plant types per week had more diverse microbiomes than those eating 10 or fewer, and also carried fewer antibiotic-resistance genes.1 "Plants" here is generous: vegetables, fruit, wholegrains, legumes, nuts, seeds, herbs and spices all count, and variety matters more than quantity because different plants carry different fibres and polyphenols.
The mechanism is reasonably well understood. Most fibres and many polyphenols reach the colon undigested, where microbes ferment them into short-chain fatty acids (SCFAs): mainly acetate, propionate and butyrate. Butyrate is the preferred fuel for the cells lining the colon and helps regulate the immune system and the gut barrier.3 Crucially, different microbes specialise in different fibres, so a varied plant diet feeds a broader range of species. A human trial by Holscher and colleagues in mBio (2019) showed that distinct fermentable fibres produced different shifts in microbiota and SCFA output, with resistant starch giving the largest butyrate rise.8
| Food / fibre | What it provides | Tends to support | Evidence note |
|---|---|---|---|
| Onions, leeks, garlic, chicory | Inulin / fructans (prebiotic fibre) | Bifidobacterium, SCFA production | Human trials show bifidogenic effect; can cause wind at first. |
| Oats, barley | Beta-glucan, mixed fibres | SCFA producers; also lowers cholesterol | Strong, consistent human data for fibre benefits. |
| Cooked-and-cooled potato, rice, legumes | Resistant starch | Butyrate producers | Resistant starch gave the largest butyrate rise in trials.8 |
| Beans, lentils, chickpeas | Fibre, resistant starch, polyphenols | Broad fibre-fermenting community | Among the most fibre-dense foods; observational links to diversity. |
| Berries, cocoa, green tea, coffee | Polyphenols | Polyphenol-metabolising microbes | Mechanistic and observational; causal human data thinner than for fibre. |
| Nuts, seeds | Fibre, polyphenols, fats | SCFA producers | Associated with higher diversity in cohort studies. |
The honest summary: the evidence that a varied, high-fibre plant diet supports a richer microbiome and more SCFA production is one of the stronger findings in the whole field. The precise "30" is a memorable rule of thumb rather than a magic threshold, but the underlying principle of plant variety is sound.
Fermented foods: the Stanford study
The most discussed recent trial is the Stanford fermented-foods study, led by Hannah Wastyk and Gabriela Fragiadakis, with Justin and Erica Sonnenburg and Christopher Gardner as senior authors, published in Cell in 2021.2 Thirty-six healthy adults were randomised for 10 weeks to a diet high in fermented foods (yoghurt, kefir, fermented cottage cheese, kimchi and other fermented vegetables, vegetable-brine drinks and kombucha) or a diet high in fibre.
The fermented-foods group showed an increase in overall microbiome diversity, with bigger servings giving stronger effects, and a fall in 19 inflammatory proteins in the blood, including interleukin-6. Strikingly, the high-fibre arm did not raise diversity over the same 10 weeks, and in people who started with low diversity, fibre was linked to a rise in some inflammatory markers. The authors suggested that a fibre-poor microbiome may need a longer run-up, or the right microbes present, before it can use extra fibre well.
Read this carefully. This was a small, short trial in healthy adults and the findings need replication before anyone treats fermented foods as a guaranteed anti-inflammatory. It does not mean fibre is unhelpful; the wider evidence for fibre is far larger. It does suggest fermented foods are a low-risk, promising addition, and that the two strategies may work through different routes.
What damages diversity
Three things have reasonably consistent human evidence behind them.
- Ultra-processed, low-fibre diets. A diet built on refined, packaged foods starves fibre-fermenting microbes. A 2022 Gastroenterology feeding study by Chassaing and colleagues found the common emulsifier carboxymethylcellulose, added to an otherwise additive-free diet, reduced microbial richness and depleted Faecalibacterium prausnitzii, a key butyrate producer.4 Reviews link the broader rise in ultra-processed food to reduced diversity and a weaker gut barrier, though much of that evidence is still observational or preclinical.9
- Unnecessary antibiotics. Antibiotics are sometimes essential and you should never skip a course your doctor judges necessary. But they hit the microbiome hard. In a 2018 Nature Microbiology study, Palleja and colleagues gave 12 healthy men a short course of three strong antibiotics; diversity largely recovered within about six weeks, but nine common beneficial species were still missing after six months, while some less desirable microbes had moved in.10 This is the case for avoiding antibiotics you do not actually need, not for refusing ones you do.
- Very low-fibre diets generally. Animal work from the Sonnenburg lab has shown that low fibre across generations can permanently erode diversity, and human fibre intake in the UK sits well below the recommended 30 g a day for most adults. Less fibre means fewer SCFAs and a thinner, less diverse community.
The honest limits of tests and probiotics
This is where the gap between marketing and evidence is widest, so it is worth being blunt.
At-home microbiome tests. These promise to map your gut and tell you what to eat or supplement. The problem is reproducibility. When researchers sent identical stool samples to seven different consumer testing companies, the results, and the health advice that followed, were dramatically different from one another.5 A 2024 international consensus statement in The Lancet Gastroenterology & Hepatology concluded there are currently no validated, broadly accepted clinical microbiome tests, and that patients and clinicians should not use them to plan treatment.11 A snapshot of your gut also shifts within days of changing your diet, so a one-off score has limited meaning. For most people, the money is better spent on more varied food than on a test.
Most probiotic supplements. Specific probiotic strains have good evidence for specific situations, for example reducing antibiotic-associated diarrhoea. But the broad claim that an over-the-counter probiotic will "boost your diversity" is largely unsupported: most studied probiotics are transient visitors that do not durably colonise an adult gut, and effects are strain-specific, so one product's results do not transfer to another. Fermented foods performed better than a fibre diet for diversity in the Stanford trial, which is a different thing from a capsule. Our broader take on supplement claims, and how to avoid paying for hope, sits in the health library and across our insights.
Practical, food-first steps
If you take the evidence at face value, the to-do list is refreshingly cheap and low-risk. Note that this is general information, not personal medical advice.
- Chase plant variety, not just quantity. Aim toward 30 different plants a week. Tinned beans, frozen vegetables, herbs, spices, nuts and seeds all count, so this is achievable on a normal UK budget.
- Build fibre up slowly. Going from low to high fibre overnight causes bloating and wind. Add one or two new plants a week and let your microbes adapt, especially if you start with a low-fibre diet.
- Add a small daily fermented food. Live yoghurt, kefir, kimchi or sauerkraut. Choose unpasteurised or "live" versions where possible; shelf-stable jarred kraut is often pasteurised and contains few live microbes.
- Cut back on ultra-processed staples, not every treat. Swapping a few refined items a day for whole foods does more than any supplement.
- Only take antibiotics you need, and always finish a course your doctor prescribes.
What to ask your GP
- Are these digestive symptoms worth investigating, rather than something I should manage with diet alone?
- Is this antibiotic prescription genuinely necessary, and is there a narrower-spectrum option?
- I have a diagnosed gut condition (IBD, coeliac, IBS): how does that change the "eat more fibre" advice for me?
- Should I be referred to a dietitian rather than relying on a commercial gut test?
References
- McDonald D, Hyde E, Knight R, et al. American Gut: an open platform for citizen science microbiome research. mSystems. ASM, 2018.
- Wastyk HC, Fragiadakis GK, Sonnenburg JL, Gardner CD, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. Cell, 2021.
- Silva YP, et al. The role of short-chain fatty acids from gut microbiota in gut-brain communication and health. Front Endocrinol. PMC6433893, 2020.
- Chassaing B, Gewirtz AT, et al. Randomized controlled-feeding study of dietary emulsifier carboxymethylcellulose reveals detrimental impacts on the gut microbiota and metabolome. Gastroenterology. PMID 34774538, 2022.
- Scientific American. Scientists gave the same sample to seven at-home microbiome tests; the results were dramatically different. scientificamerican.com, 2026 (reporting on Communications Biology).
- Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. BMJ 2018;361:k2179, 2018.
- Asnicar F, Berry SE, Segata N, Spector TD, et al. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat Med. Nature Medicine, 2021.
- Deehan EC, Holscher HD, Walter J, et al. Dynamics of human gut microbiota and short-chain fatty acids in response to dietary interventions with three fermentable fibers. mBio. mBio, 2019.
- Whelan K, et al. Ultra-processed foods and food additives in gut health and disease. Nat Rev Gastroenterol Hepatol. Nature Reviews, 2024.
- Palleja A, Mikkelsen KH, Forslund SK, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol. Nature Microbiology, 2018.
- Porter J, et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol. The Lancet Gastroenterology & Hepatology, 2024.
This article is educational and does not constitute medical advice, diagnosis, or a treatment recommendation. Medication uses described as “off-label” are not licensed for that purpose in the UK and should only be considered under qualified clinical supervision. Always speak to your GP, pharmacist, or a registered specialist before starting, stopping, or changing any treatment. If you have severe or alarm symptoms - unintentional weight loss, blood in your stool, difficulty swallowing, persistent vomiting, a fever, or severe pain - seek urgent medical care.