Goal · Gut microbiome
Food and the gut microbiome: fiber, fermented foods and probiotics
Microbiome science is young. A varied, fiber-rich diet is sensible on many grounds, one small trial found fermented foods raised microbe diversity, and probiotic evidence is strain- and condition-specific.
By the editors of Alimentotherapy Last reviewed 4 min read Not medical advice
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The short answer
The best direct evidence is one small randomized trial: over 17 weeks, healthy adults who ate more fermented foods had steadily rising gut microbe diversity and lower inflammatory markers, while a high-fiber diet left diversity unchanged Wastyk 2021. Beyond that, "a healthy microbiome" is not something a test or a product can yet define, so the practical advice is the same as for regularity and heart health: more fiber from a wide range of plants MedlinePlus.
Foods and herbs for gut microbiome, graded
Every claim from our remedy pages that relates to gut microbiome, strongest evidence first. Each row links to the full page and its sources.
| Food or herb | Grade | What the research found |
|---|---|---|
| ProbioticsChanging the gut microbiome in healthy adults | Not supported | A systematic review of seven placebo-controlled trials in healthy adults found no effect of probiotic supplements on fecal microbiota diversity, richness or evenness; only one trial found a change in overall community structure. |
What is known, and what is not
Trillions of microbes live in the gut, and diet is one of the strongest influences on which ones thrive. Much of the research is in mice or is observational. The American Gut project, with samples from more than 10,000 citizen scientists, linked the variety of plants people ate to the make-up of their gut microbes and found that broad labels such as "vegan" explained little Mcdonald 2018. Studies like this show associations, not that changing your diet changes your health through the microbiome.
Be wary of home microbiome tests and products that claim to "rebalance" your gut. There is no agreed definition of a healthy microbiome to measure against, and a single stool sample shifts with yesterday's meals.
Fiber, from many plants
Gut bacteria ferment fiber the body cannot digest. Americans eat about 16 grams a day on average, against a recommendation of 21 to 38 grams for older children and adults MedlinePlus. Add it gradually over a few weeks, with enough fluid, to avoid gas and stomach upset MedlinePlus.
In the Stanford trial, the high-fiber group's microbes produced more fiber-digesting enzymes, but their diversity did not rise within 17 weeks, and their immune responses split into different patterns depending on how diverse their microbes were at the start Wastyk 2021. Fiber has strong evidence for regularity, cholesterol and blood sugar regardless; see regularity. Beans and lentils, oats, nuts, berries and vegetables are easy ways to widen the range. A food diary such as Cronometer shows how much fiber you eat now.
Fermented foods
Wastyk and colleagues randomized 36 healthy adults (18 per group) to a high-fiber or a high-fermented-food diet for 17 weeks. The fermented-food group showed a steady rise in microbe diversity and a fall in inflammatory markers. The trial's primary immune measure did not change in either group Wastyk 2021. It is promising, and it is one small trial without health outcomes.
Yogurt and kefir and fermented vegetables have their own graded pages. Kombucha is the least studied: a 2019 systematic review found only one study of kombucha's effects in people, against many claims from lab and animal work Kapp 2019. If you want to make ferments at home, follow a tested method: home fermentation, sauerkraut, kimchi, milk kefir and kombucha.
Probiotic supplements
Probiotics are live microorganisms intended to have a health benefit. NCCIH notes they have shown promise for some specific uses, such as lowering the chance of diarrhea with antibiotics, but results depend on the strain and the condition, and for irritable bowel syndrome reviewers could not say which species or strains help NCCIH. Whether healthy people gain anything from a daily probiotic is unproven. The probiotics page grades the main uses.
Safety
Probiotics appear safe for most healthy people, but severe or fatal infections have been reported in premature infants given probiotics, and NCCIH flags people who are very ill or have weakened immune systems as an exception NCCIH. Ask your clinician first in those cases.
When to see a clinician, not the pantry
- Blood in the stool, black or tarry stools, or losing weight without trying.
- Diarrhea lasting more than a few days, or diarrhea after a course of antibiotics, especially with fever or belly pain.
- A change in bowel habits that lasts for weeks.
- Before taking probiotics if you are very ill, have a weakened immune system, or for a premature baby.
Common questions
Do fermented foods improve gut health?
One small Stanford trial suggests they may change the microbiome: 18 healthy adults eating more fermented foods for 17 weeks had rising gut microbe diversity and lower inflammatory markers. It is a single trial without health outcomes, so treat it as promising rather than proven.
Should I take a probiotic?
Most healthy people have no proven need. NCCIH says probiotics show promise for specific uses such as diarrhea with antibiotics, but benefits depend on the strain and condition. Premature infants and people who are very ill or have weakened immune systems should ask a clinician first.
Is kombucha good for your gut?
Nobody knows yet. A 2019 systematic review found only one study of kombucha's effects in people; the health claims come from lab and animal work. Enjoy it as a drink if you like it, not as a health product.
Sources
Primary research and government sources, each checked on the date this page was reviewed.
- PubMedWastyk HC, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021. PMID 34256014.
- PubMedMcDonald D, et al. American Gut: an open platform for citizen science microbiome research. mSystems. 2018. PMID 29795809.
- PubMedKapp JM, Sumner W. Kombucha: a systematic review of the empirical evidence of human health benefit. Ann Epidemiol. 2019. PMID 30527803.
- NCCIHNational Center for Complementary and Integrative Health. Probiotics: Usefulness and Safety.
- MedlinePlusMedlinePlus. Fiber.
Keep reading
- RemedyFermented foodsSauerkraut, kimchi, miso, kefir and kombucha. One well-run trial suggests eating more of them changes the gut microbiome; claims beyond that are mostly untested in people.
- RemedyYogurt and kefirCultured milks with the clearest evidence of any fermented food: their live bacteria help digest lactose. Other claims rest on probiotic supplement trials or observational data.
- RemedyProbioticsLive microbes sold as supplements and found in some fermented foods. Trials support specific uses alongside antibiotics; most other claims are unproven, and effects depend on the strain.
- Kitchen practiceFermentationThe oldest way to keep vegetables through winter. A tested method, the right salt and clean equipment make it safe; the health claims are more modest than the hype.
- ComparisonKombucha vs kefirBoth are fizzy fermented drinks, but they start from different things: kombucha from sweet tea, kefir from milk (or sugar water for water kefir). Kefir has a little human evidence; kombucha has nearly none.
- GoalFood for regularity: fiber, fluids, kiwifruit and prunesMost adults eat well under the fiber they need. Raising it slowly, with fluid, is the first step; kiwifruit, prunes and psyllium all have trial support.