How to Increase Microbiome Diversity

Medically reviewed and written by Dr Zeeshan Afzal (MBBS), Medical Officer at Welzo. Last updated: July 2026. This article is for general information and does not replace individual medical advice.

If you want to increase gut bacteria diversity, the single most reliable lever you have is what lands on your plate over the next few weeks. A more diverse gut microbiome — meaning a greater number of different bacterial species, more evenly distributed — is consistently associated with better metabolic health, a stronger gut barrier function, a better-regulated immune response and greater resilience after illness or antibiotics. Low diversity, by contrast, is a recurring feature of gut dysbiosis, inflammatory bowel disease, obesity and type 2 diabetes.

This guide explains what microbiome diversity actually is, what erodes it, and the evidence-based steps that raise it — from the 30-plants-a-week target to fermented foods, fibre, exercise and sleep. You will also find where targeted supplements genuinely help. Welzo's gut health range and probiotics collection include several of the categories discussed here, including Akkermansia muciniphila, modified citrus pectin powder, Welzo Ultra Purity Berberine and Welzo Ultra Purity TUDCA. For the wider picture, start with our pillar guide to gut health in the UK and our overview of microbiome diversity.

Table of Contents

• What Gut Bacteria Diversity Actually Means
• Why Increasing Gut Bacteria Diversity Matters
• What Reduces Microbiome Diversity
• 12 Evidence-Based Ways to Increase Gut Bacteria Diversity
• An 8-Week Diversity Plan
• Supplements That Support Diversity
• How to Measure Your Progress
• How Long Does It Take?
• Common Mistakes to Avoid
• When to See a Doctor
• Frequently Asked Questions
• References

What Gut Bacteria Diversity Actually Means

Image: Gut microbiota illustration, Wikimedia Commons, CC BY 4.0.

The adult large intestine houses somewhere in the order of 10 to 100 trillion micro-organisms, spanning hundreds of bacterial species plus archaea, fungi and viruses. "Diversity" is a specific ecological measurement of that community — not a vague wellness term.

Alpha diversity vs beta diversity

Alpha diversity describes the variety within your own gut. It is what most microbiome tests report, usually as a Shannon index or an observed-species count. Beta diversity compares your microbiome to someone else's — it measures how different two communities are. When people talk about wanting to increase gut bacteria diversity, they almost always mean raising alpha diversity.

Richness and evenness

Alpha diversity has two components. Richness is simply how many different species are present. Evenness is how balanced their numbers are. A gut with 200 species where three dominate 80% of the population is less healthy than a gut with 200 species spread more evenly. This is why an overgrowth of a single organism — as in candida overgrowth or SIBO — can coincide with a technically "rich" but functionally poor microbiome.

Diversity is a marker, not the goal itself

It is important to be precise here, because a lot of marketing is not. Higher diversity is associated with better health outcomes in population studies, but it is a proxy for what really matters: a microbial community with the metabolic capacity to ferment fibre, produce short-chain fatty acids, maintain the mucus layer and resist colonisation by pathogens. Diversity is the fingerprint of that capacity, not the mechanism. A person recovering from a serious infection can show a temporary diversity spike that means nothing good.

Why Increasing Gut Bacteria Diversity Matters

Short-chain fatty acid production

Different bacteria ferment different substrates. A diverse community can break down a broader range of fibres, producing more acetate, propionate and — critically — butyrate. Butyrate is the primary fuel for colonocytes, the cells lining your colon, and it helps regulate inflammation and tight-junction integrity. You can read more in our guides to short-chain fatty acids and butyrate supplements.

Gut barrier and mucus layer

Specialist organisms such as Akkermansia muciniphila live in and maintain the intestinal mucus layer. When diversity falls, mucus-layer maintenance suffers, which is one plausible mechanism behind increased intestinal permeability — the phenomenon popularly called leaky gut. We discuss the evidence honestly in is leaky gut real? and gut barrier function.

Immune regulation and colonisation resistance

A dense, diverse community occupies ecological niches and competes for nutrients, making it harder for pathogens such as Clostridioides difficile or Salmonella to establish. This is the principle behind using probiotics for C. diff risk and traveller's diarrhoea prevention. Diversity also shapes immune tolerance — see gut health and the immune system and gut health and autoimmunity.

Metabolic, hormonal and mental health links

Lower diversity has been repeatedly associated with insulin resistance, higher visceral fat and adverse lipid profiles. It also intersects with the gut-brain connection, hormone metabolism, skin health, sleep and blood sugar regulation.

What Reduces Microbiome Diversity

Before adding, it is worth removing. These are the best-documented drivers of low diversity.

Two of these deserve emphasis. First, antibiotics: in the American Gut Project, participants who had taken antibiotics in the previous month had less diverse microbiomes than those who had taken none in the previous year. Second, acid suppression: a large twin study and subsequent meta-analyses found lower microbial diversity in regular proton pump inhibitor users, with depletion of short-chain fatty acid-producing families. Neither finding means you should stop a prescribed medicine — it means the decision to continue long-term should be a deliberate one made with your prescriber. Similar considerations apply to metformin, NSAIDs and iron supplements.

12 Evidence-Based Ways to Increase Gut Bacteria Diversity

1. Eat 30 or more different plants a week

Image: Fruit and vegetable basket, Wikimedia Commons, Public Domain Mark 1.0.

This is the highest-yield intervention and the one with the clearest signal. The American Gut Project — a citizen-science study of more than 10,000 participants across the US, UK and Australia — found that people eating more than 30 different plant types per week had measurably more diverse gut microbiomes than those eating 10 or fewer, and that this held regardless of whether they identified as omnivore, vegetarian or vegan.

What counts as a plant point

Fruit, vegetables, wholegrains, legumes, nuts, seeds, herbs and spices all count. Different varieties of the same species count separately in practice (red versus white onion, for instance), while a repeated food counts only once per week. Herbs and spices count as quarter points in most versions of the challenge. Our full guide to eating 30 plants a week includes a tracking template, and the best foods for gut health lists the highest-value additions.

The fastest way to get there

Mixed seed blends, tinned mixed beans, frozen mixed vegetables and a rotating spice jar will add 10–15 points a week for very little effort or expense. Buying "four bean mix" instead of a single bean is four points instead of one.

2. Reach 30g of fibre per day

Image: Mixed vegetables, Wikimedia Commons, CC BY 3.0.

The UK Scientific Advisory Committee on Nutrition sets the adult target at 30g of fibre daily. Most of us fall well short: national survey data indicate average intakes around 19–20g, with roughly 9% of adults meeting the recommendation. That gap is, in microbial terms, a chronic food shortage.

Vary the type, not just the amount

Different fibres feed different organisms, so variety matters as much as total grams. Include soluble/viscous fibres (oats, psyllium, apples, citrus pectin), insoluble fibres (wholegrains, skins, nuts), resistant starch (cooled potato, rice and pasta, green banana) and fermentable oligosaccharides (onion, garlic, leek, chicory root). See how to increase fibre, high-fibre foods in the UK and psyllium vs inulin.

Go slowly if you bloat

Increasing fibre by 5g per week rather than all at once dramatically reduces gas and discomfort. If bloating persists, read foods that cause bloating and trapped wind relief.

3. Add fermented foods daily

Image: Sauerkraut, Wikimedia Commons, CC BY-SA 3.0.

A randomised trial at Stanford School of Medicine assigned 36 healthy adults to a 10-week diet high either in fermented foods or in fibre. The fermented-food group showed an increase in overall microbial diversity, with larger effects at larger servings, alongside decreases in a set of inflammatory proteins. Notably, the high-fibre arm did not increase diversity over that timeframe — the researchers concluded that raising fibre alone over a short period was insufficient to shift diversity.

This does not mean fibre is unimportant; it means fibre works over a longer horizon and fermented foods act faster. Do both. Aim for 2–4 servings a day of live yoghurt, kefir, sauerkraut, kimchi, miso, tempeh or kombucha. Our guides to fermented foods in the UK and fermented food vs probiotics cover which supermarket products are actually live.

4. Prioritise prebiotic foods

Prebiotics are the substrates your existing bacteria ferment. The richest sources are onions, garlic, leeks, asparagus, chicory root, Jerusalem artichoke, slightly green bananas, oats and barley. See prebiotic foods and prebiotic vs probiotic.

5. Include resistant starch

Cooking and then cooling starchy foods converts some starch into a form that resists digestion and reaches the colon intact, where it preferentially feeds butyrate producers. Cooked-and-cooled potatoes, rice, pasta and oats all qualify — and reheating does not undo the effect. Read resistant starch.

6. Eat polyphenol-rich foods

Only around a tenth of dietary polyphenols are absorbed in the small intestine; the rest reach the colon and are metabolised by gut bacteria into bioactive compounds. Berries, extra virgin olive oil, green tea, coffee, cocoa, red grapes and herbs are the densest sources. See polyphenols and gut health.

7. Use a multi-strain probiotic strategically

Probiotics do not usually colonise permanently, and most will not raise your alpha diversity score directly. What they can do is provide transient functional benefit — modulating immunity, producing metabolites, competing with pathogens and supporting recovery after antibiotics. Multi-strain formulations have broader functional coverage than single strains; see single vs multi-strain probiotics, how to choose a probiotic and browse the Welzo probiotics collection. Strain-specific guides include Lactobacillus rhamnosus GG, Bifidobacterium longum, Lactobacillus plantarum, Bacillus coagulans and Saccharomyces boulardii.

8. Consider next-generation and spore-based strains

Akkermansia muciniphila is a mucin-degrading species that is generally more abundant in people who exercise regularly and less abundant in metabolic disease. It sits outside the traditional Lactobacillus/Bifidobacterium categories and is available as a standalone Akkermansia supplement. Compare approaches in Akkermansia vs probiotics, pasteurised Akkermansia and spore-based probiotics.

9. Exercise regularly — and keep doing it

Cross-sectional work first flagged this: professional rugby players were found to have greater alpha diversity than sedentary controls matched for age and BMI, and physically active women carry higher levels of butyrate producers such as Faecalibacterium prausnitzii and Roseburia hominis, plus more Akkermansia muciniphila. A 2024 meta-analysis of 25 exercise-intervention studies in 1,044 participants found a small but statistically significant increase in Shannon diversity with exercise, with larger effects in women and older adults.

Two caveats worth stating plainly. Effects are modest and inconsistent across trials, and they appear to reverse when people return to being sedentary — consistency matters more than intensity. See gut health for athletes and, if intense training upsets your stomach, runner's trots.

10. Protect your sleep and circadian rhythm

Gut bacteria have their own daily rhythms, entrained partly by your meal timing. Irregular sleep and late-night eating blunt those oscillations. Practical steps: a consistent wake time, morning daylight, and a 12-hour overnight fast where feasible. See gut health and sleep.

11. Manage chronic stress

Stress alters gut motility, secretions and bile flow, which changes the environment your bacteria live in. Breathwork, time outdoors and structured exercise all help via vagal tone — see the vagus nerve and the gut and probiotics for anxiety.

12. Get outdoors and reduce unnecessary sterility

Environmental microbial exposure — gardening, contact with soil, being around animals, spending time in green space — is associated with greater microbial diversity. Washing raw produce rather than peeling everything, and avoiding antibacterial products where plain soap will do, are small but sensible adjustments.

An 8-Week Diversity Plan

If you prefer a structured protocol, see our gut reset protocol and the companion guide on increasing gut bacteria diversity.

Supplements That Support Diversity

Image: Kefir, Wikimedia Commons, CC BY-SA 3.0.

Supplements are an adjunct to diet, not a substitute for it. That said, several categories have a reasonable evidence base and a clear rationale.

Practical questions such as when to take probiotics, how long they take to work, whether they need refrigeration and CFU vs AFU are covered in detail elsewhere on the site. Safety information is in probiotics safety and probiotic side effects.

How to Measure Your Progress

Symptom and habit tracking

The cheapest and most useful measures are free: weekly plant-point count, daily fibre estimate, stool form and frequency, bloating scores and energy. Most people notice change in these before any laboratory marker moves.

Microbiome testing

Consumer sequencing tests report alpha diversity, relative abundances and sometimes SCFA-producer estimates. They are useful for tracking direction of travel over months but are not diagnostic, and results vary between providers and even between samples. Compare options in our microbiome test comparison, gut microbiome test UK guide and stool test guide.

Clinical tests that matter more

If you have symptoms, clinically validated tests are more informative than diversity scores: faecal calprotectin for inflammation, coeliac serology, H. pylori testing, SIBO breath testing and a general blood panel.

How Long Does It Take?

Common Mistakes to Avoid

Chasing a diversity number

Optimising a test score rather than your symptoms and overall diet is a poor use of effort. Diversity is a marker of a functioning ecosystem, not a target in itself.

Increasing fibre too quickly

Jumping from 15g to 35g overnight reliably produces bloating and often causes people to abandon the whole project. Ramp gradually and drink enough fluid.

Staying on a low-FODMAP diet indefinitely

The elimination phase of the low-FODMAP diet is intended to last 4–6 weeks. Prolonged restriction reduces the substrates available to your microbiome and can lower diversity. Reintroduction is the point — see FODMAP reintroduction and IBS types.

Assuming more probiotics is better

Higher CFU counts are not linearly better, and there is such a thing as too many probiotics. Strain selection and evidence for the specific indication matter more than dose. See also do probiotics work?

Ignoring red-flag symptoms while "working on the gut"

This is the most important one, and it leads to the next section.

When to See a Doctor

Improving microbiome diversity is a wellness goal, not a treatment for undiagnosed disease. Please arrange an urgent GP appointment — do not self-manage with diet or supplements — if you have any of the following:

• Blood in your stool, or black tarry stools
• Unexplained weight loss
• A persistent change in bowel habit lasting more than three weeks, particularly if you are over 50
• Difficulty swallowing, or persistent vomiting
• Abdominal or rectal masses, or persistent unexplained abdominal pain
• Iron-deficiency anaemia without an obvious cause
• Night-time symptoms that wake you, or fever with abdominal pain
• A family history of bowel cancer, coeliac disease or inflammatory bowel disease alongside new symptoms

See when to see a GP about stomach symptoms and bowel cancer screening in the UK. If you are pregnant, immunocompromised, have a central venous catheter, or have a diagnosed condition such as Crohn's disease or ulcerative colitis, discuss probiotics and prebiotics with your clinician before starting.

Frequently Asked Questions

How can I increase gut bacteria diversity quickly?

The fastest evidence-backed route is adding fermented foods. In a 10-week randomised trial at Stanford, a high fermented-food diet increased microbial diversity, with larger servings producing stronger effects. Combine that with a steady climb toward 30 different plant foods a week — but expect meaningful change over weeks, not days.

What is a good gut microbiome diversity score?

There is no universally agreed cut-off, and scores are not comparable between testing companies because they use different sequencing methods and reference databases. What is more useful is your own trend over time on the same test, interpreted alongside your symptoms. Treat any single number with caution.

Do probiotics increase microbiome diversity?

Usually not directly. Most probiotic strains are transient and do not permanently colonise, so they rarely raise alpha diversity on a test. They can still provide real functional benefits — supporting recovery after antibiotics, easing certain IBS symptoms and competing with pathogens. Prebiotics and dietary variety are the better tools for diversity itself.

How long does it take to increase gut bacteria diversity?

Composition starts shifting within 24–72 hours of a major dietary change, but a measurable, durable diversity change generally takes 4–12 weeks of consistent eating. Recovery after a course of antibiotics can take six months or longer, and may not return fully to baseline.

Does fibre alone increase gut bacteria diversity?

Not necessarily over short periods. The Stanford trial found that a high-fibre diet did not raise diversity over 10 weeks, though it did produce other favourable changes. Fibre remains essential for short-chain fatty acid production and long-term microbial function — it simply works more slowly than fermented foods on this particular measure.

Can antibiotics permanently reduce microbiome diversity?

A single short course usually causes a temporary drop with substantial recovery over weeks to months. Repeated or broad-spectrum courses can produce longer-lasting reductions, and some species may not return. Supporting recovery with fibre, fermented foods and appropriate probiotics is sensible — see our guide to probiotics after antibiotics.

Does exercise increase gut bacteria diversity?

Modestly. A 2024 meta-analysis of 25 intervention studies found a small but statistically significant increase in Shannon diversity with exercise, with larger effects in women and older adults. Athletes show higher diversity than sedentary controls. Effects appear to fade if you stop, so consistency matters more than intensity.

Do I need a microbiome test before making changes?

No. The interventions that raise diversity — more plants, more fibre, fermented foods, exercise, better sleep — are safe and beneficial regardless of your baseline. A test is optional and most useful if you want an objective before-and-after, or if you are working with a clinician on a specific problem.

Can you have too much microbiome diversity?

Very high diversity is not automatically good. It can occasionally reflect an unstable community or colonisation by organisms that do not belong in the colon, and diversity can rise transiently during illness. A stable, functional community producing adequate short-chain fatty acids matters more than a high score.

What single change makes the biggest difference to gut bacteria diversity?

Increasing the variety of plant foods you eat, rather than the quantity of any one of them. The American Gut Project data showed that people eating more than 30 plant types weekly had more diverse microbiomes than those eating fewer than 10, independently of their overall dietary pattern. If you change one thing, change that.

References

1. McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18. https://doi.org/10.1128/msystems.00031-18
2. University of California San Diego. What's in Your Gut? — American Gut Project findings. https://today.ucsd.edu/story/whats-in-your-gut
3. ScienceDaily. Big data from world's largest citizen science microbiome project. 2018. https://www.sciencedaily.com/releases/2018/05/180515092931.htm
4. Stanford Medicine. Fermented-food diet increases microbiome diversity, decreases inflammatory proteins. 2021. https://med.stanford.edu/news/all-news/2021/07/fermented-food-diet-increases-microbiome-diversity-lowers-inflammation.html
5. British Nutrition Foundation. Fibre — Nutrition Information. https://www.nutrition.org.uk/nutritional-information/fibre/
6. HEART UK. Fibre and wholegrain recommendations. https://www.heartuk.org.uk/dietary-recommendations/fibre-recommendations
7. Hooper B, et al. 30 g of fibre a day: An achievable recommendation? Nutrition Bulletin. 2015. https://onlinelibrary.wiley.com/doi/full/10.1111/nbu.12141
8. Increasing fibre intake in the UK: lessons from the Danish Whole Grain Partnership. Nutrition Bulletin / PMC. https://pmc.ncbi.nlm.nih.gov/articles/PMC10803819/
9. Effects of Exercise on Gut Microbiota of Adults: A Systematic Review and Meta-Analysis. Nutrients. 2024;16(7):1070. https://pmc.ncbi.nlm.nih.gov/articles/PMC11013040/
10. A systematic review on the effects of exercise on gut microbial diversity, taxonomic composition and microbial metabolites. Frontiers in Physiology. 2023. https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2023.1292673/full
11. Exercise influence on the microbiome–gut–brain axis. Gut Microbes / PMC. https://pmc.ncbi.nlm.nih.gov/articles/PMC6748614/
12. Jackson MA, et al. Proton pump inhibitors alter the composition of the gut microbiota. Gut. 2016;65(5):749–756. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4853574/
13. Meta-analysis of the effects of proton pump inhibitors on the human gut microbiota. BMC Microbiology. 2023. https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02895-w
14. Seto CT, et al. Prolonged use of a proton pump inhibitor reduces microbial diversity. Microbiome. 2014;2:42. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242847/
15. Diet Quality and the Fecal Microbiota in Adults in the American Gut Project. The Journal of Nutrition. https://www.sciencedirect.com/science/article/pii/S0022316623126216
16. Gut Microbiota for Health. Practical recommendations to increase gut microbial diversity. https://www.gutmicrobiotaforhealth.com/practical-recommendations-to-increase-gut-microbial-diversity/
17. UCLA Health. Resetting gut microbiome is a long-term project. https://www.uclahealth.org/news/article/resetting-gut-microbiome-is-a-long-term-project

About the Author

Dr Zeeshan Afzal (MBBS) is a qualified medical doctor and Medical Officer at Welzo, where he reviews and authors clinical content across digestive health, nutrition and preventive medicine. He writes with a focus on translating peer-reviewed evidence into practical, safe guidance for UK readers.

Medical Disclaimer

This article is intended for general educational purposes and does not constitute medical advice, diagnosis or treatment. Nutritional and lifestyle interventions affect individuals differently. Always speak to your GP, pharmacist or a registered dietitian before starting a new supplement, particularly if you are pregnant or breastfeeding, immunocompromised, taking prescription medication, or living with a diagnosed gastrointestinal condition. If you have any red-flag symptoms described above, seek medical assessment promptly. In an emergency, call 999 or attend your nearest A&E.