20 most important ways to support a healthy microbiome
1. Eat a high-fiber diet
This is probably the single most important dietary intervention.
Gut bacteria ferment dietary fiber into metabolites including acetate, propionate and butyrate, which influence the intestinal environment, epithelial cells and immune system.
Full reference:
Makki K, Deehan EC, Walter J, Bäckhed F. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host & Microbe. 2018;23(6):705-715. doi:10.1016/j.chom.2018.05.012.
2. Eat many different types of plant foods
Don’t get all your fiber from one supplement.
Rotate among:
- vegetables
- fruits
- legumes
- whole grains
- nuts
- seeds
- roots and tubers
- herbs and spices
Different fibers feed different microbial populations.
Full reference:
Makki K, Deehan EC, Walter J, Bäckhed F. Cell Host & Microbe. 2018;23(6):705-715.
3. Aim for adequate—not just minimal—fiber
Higher fiber intake is consistently associated with favorable microbiome effects, although individual responses vary.
A meta-analysis of 64 studies involving 2,099 healthy adults found that fiber interventions increased Bifidobacterium, Lactobacillus and fecal butyrate under some conditions.
Full reference:
So D, Whelan K, Rossi M, et al. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. American Journal of Clinical Nutrition. 2018;107(6):965-983. doi:10.1093/ajcn/nqy041.
4. Regularly eat legumes
Beans, lentils, chickpeas and peas are exceptionally useful microbiome foods because they provide fermentable fibers and resistant starches.
Full reference:
O’Grady J, O’Connor EM, Shanahan F. Review article: dietary fibre in the era of microbiome science. Alimentary Pharmacology & Therapeutics. 2019;49(5):506-515. doi:10.1111/apt.15129.
5. Eat onions, garlic, leeks and other alliums
These provide fermentable carbohydrates and prebiotic compounds, including fructans, which can be metabolized by particular beneficial microbes.
Full reference:
So D, Whelan K, Rossi M, et al. American Journal of Clinical Nutrition. 2018;107(6):965-983.
6. Eat resistant starch
Sources include:
- cooled potatoes
- cooled rice
- green bananas
- legumes
- some whole grains
Resistant starch reaches the colon and becomes a substrate for bacterial fermentation.
Full reference:
Birt DF, Boylston T, Hendrich S, et al. Resistant starch: promise for improving human health. Advances in Nutrition. 2013;4(6):587-601. doi:10.3945/an.113.004325.
7. Eat fermented foods
Examples include:
- yogurt containing live cultures
- kefir
- sauerkraut
- kimchi
- fermented vegetables
A randomized controlled trial found that a high-fermented-food diet increased microbiome diversity and decreased several inflammatory markers.
Full reference:
Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137-4153.e14. doi:10.1016/j.cell.2021.06.019.
8. Eat polyphenol-rich foods
Polyphenols occur in:
- berries
- apples
- cocoa
- tea
- coffee
- olives
- herbs
- spices
- many vegetables
Gut microbes metabolize many polyphenols, and polyphenols can in turn influence microbial ecology.
Full reference:
Cardona F, Andrés-Lacueva C, Tulipani S, Tinahones FJ, Queipo-Ortuño MI. Benefits of polyphenols on gut microbiota and implications in human health. Journal of Nutritional Biochemistry. 2013;24(8):1415-1422. doi:10.1016/j.jnutbio.2013.05.001.
9. Eat nuts and seeds
Nuts provide fiber, polyphenols and other substrates that can affect microbial metabolism.
Full reference:
Sánchez-González C, Cuervo A, et al. Nuts and gut microbiota: implications for human health. Nutrients. 2020.
10. Eat whole grains rather than predominantly refined grains
Whole grains provide diverse fibers and other compounds that can reach the colon and influence microbial metabolism.
Full reference:
Martínez I, Lattimer JM, Hubach KL, et al. Gut microbiome composition is altered by consumption of whole grains. Applied and Environmental Microbiology. 2013;79(9):3007-3014. doi:10.1128/AEM.03849-12.
11. Don’t make ultra-processed foods the foundation of your diet
A diet dominated by highly processed foods tends to provide less diverse fermentable substrate than a diverse whole-food diet.
This doesn’t mean every processed food is harmful or that you need a perfect diet.
Full reference:
Zinöcker MK, Lindseth IA. The Western diet-microbiome-host interaction and its role in metabolic disease. Nutrients. 2018;10(3):365. doi:10.3390/nu10030365.
12. Avoid unnecessary antibiotics
Antibiotics can cause substantial changes in intestinal microbial communities, sometimes lasting months or longer.
This does not mean avoiding antibiotics when you actually need them. Appropriate antibiotics save lives.
The objective is avoiding unnecessary exposure.
Full reference:
Francino MP. Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances. Frontiers in Microbiology. 2016;6:1543. doi:10.3389/fmicb.2015.01543.
13. After necessary antibiotics, return to a diverse diet
After antibiotic treatment, rebuilding a healthy microbial ecosystem is more complicated than simply taking a probiotic.
Dietary diversity and adequate fermentable substrate provide the microbiome with resources for recovery.
Full reference:
Palleja A, Mikkelsen KH, Forslund SK, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. 2018;3:1255-1265. doi:10.1038/s41564-018-0257-7.
14. Don’t assume that a probiotic is automatically beneficial
This is important.
“Probiotic” isn’t one treatment.
Effects are highly strain-specific.
Some probiotics have demonstrated benefits for particular conditions, while others have little measurable effect on the overall microbiome.
Full reference:
Zmora N, Zilberman-Schapira G, Suez J, et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2018;174(6):1388-1405.e21. doi:10.1016/j.cell.2018.08.041.
15. Get regular physical activity
Exercise is associated with changes in gut microbial composition and metabolic activity.
Some studies suggest physically active people have greater microbial diversity, although diet, body composition and other lifestyle factors make this difficult to separate completely.
Full reference:
Monda V, Villano I, Messina A, et al. Exercise modifies the gut microbiota with positive health effects. Oxidative Medicine and Cellular Longevity. 2017;2017:3831972. doi:10.1155/2017/3831972.
16. Maintain a healthy body composition
Obesity and metabolic dysfunction are associated with alterations in gut microbial ecology.
Improving metabolic health can therefore also improve the host environment in which the microbiome operates.
Full reference:
Leone V, Gibbons SM, Martinez K, et al. Effects of bariatric surgery on human gut microbiota. Nature Reviews Gastroenterology & Hepatology. 2015.
17. Get adequate sleep and maintain circadian regularity
The gut microbiome has its own daily rhythms, and sleep/circadian disruption can alter host–microbe interactions.
Full reference:
Thaiss CA, Zeevi D, Levy M, et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell. 2014;159(3):514-529. doi:10.1016/j.cell.2014.09.006.
18. Avoid chronic extreme dieting
Repeated severe dietary restriction can dramatically alter the substrates available to gut microbes.
A sustainable, diverse diet is generally more microbiome-friendly than cycling between extreme diets.
Full reference:
David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559-563. doi:10.1038/nature12820.
19. Maintain a healthy intestinal barrier
A healthy microbiome and healthy intestinal lining support each other.
Fiber-derived microbial metabolites such as butyrate are important for colonic epithelial physiology.
Full reference:
Parada Venegas D, De la Fuente MK, Landskron G, et al. Short chain fatty acids-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Frontiers in Immunology. 2019;10:277. doi:10.3389/fimmu.2019.00277.
20. Increase dietary diversity gradually if your current diet is low in fiber
This is one of the most practical points.
If someone currently eats very little fiber, suddenly adding enormous quantities of beans, onions, resistant starch and fiber supplements can cause:
- gas
- bloating
- abdominal discomfort
- diarrhea or constipation
Instead, increase plant diversity and fiber progressively.
The microbiome’s response to fiber is highly individual, depending partly on the person’s starting microbial ecosystem.
Full reference:
Delzenne NM, Bindels LB, Neyrinck AM, Walter J. The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer. Nature Reviews Microbiology. 2025;23:225-238. doi:10.1038/s41579-024-01108-z.
My Top Seven:
1. Eat lots of different plant foods
2. Get adequate fiber
3. Regularly eat legumes
4. Include fermented foods if tolerated
5. Minimize unnecessary antibiotics
6. Exercise regularly
7. Maintain good sleep/circadian habits
The fiber point is especially strong. A 2025 Nature Reviews Microbiology review emphasizes that dietary fibers are key substrates for the gut microbiome, but also notes that responses vary substantially among individuals and that “more diversity” isn’t necessarily the only or best endpoint.
A particularly good practical strategy
beans/lentils + vegetables + fruit + berries + whole grains + nuts/seeds + herbs/spices + onions/garlic + resistant starch + fermented foods.
That supplies the microbiome with many different substrates.”
Some oppose probiotics and prebiotics and appear to be stuck in 1980; they criticize using “1-2 bacteria.” My two have 60 bacterial strains and 15 organic respected prebiotics. This is 1 trillion CFUs and with this type of product no one has had C. diff infections with severe diarrhea in 33 years.
And one important correction to a common internet claim: a stool microbiome test showing low levels of a particular bacterium does not automatically mean that bacterium needs to be supplemented. Microbiome composition is highly individual, and current evidence is much stronger for improving the ecology and function of the microbiome through diet and lifestyle than for chasing a particular “ideal” bacterial percentage.