Gut microbiome explained simply: it is the trillions of bacteria, fungi, viruses and other microbes living in your digestive tract, mostly in your large intestine. They help break down fiber, make some vitamins and help train your immune system. Eating a wide variety of fiber-rich plant foods is the habit the sources we checked most consistently recommend.
This is general information, not medical advice. Talk to your doctor or pharmacist about your own situation.
The Harvard T.H. Chan School of Public Health describes the microbiome as trillions of microorganisms from thousands of species, including bacteria, fungi, parasites and viruses. The largest numbers live in the small and large intestines. Cleveland Clinic says your gut holds over a thousand species of bacteria alone, and that most gut microbes live in the large intestine (colon), where many are bacteria that need a low-oxygen environment. The National Institute of Environmental Health Sciences (NIEHS) notes there are as many microbes as there are human cells in the body.
Your microbiome is unique to you. Cleveland Clinic explains that babies get their first gut microbes during vaginal birth or breastfeeding, and diet and other exposures add new ones later. NIEHS says a person's core microbiome forms in the first years of life but can change over time with diet, medicines and the environment.
Digest fiber. Gut bacteria break down certain complex carbohydrates and fibers your body cannot digest on its own, producing short-chain fatty acids that feed the cells of your gut lining (Cleveland Clinic).
Make vitamins. Gut bacteria provide enzymes needed to make certain vitamins, including B1, B9, B12 and K (Cleveland Clinic). Harvard notes that the key enzymes to form vitamin B12 are found only in bacteria. Our guide to what vitamins do explains why those matter.
Recycle bile. Bacteria help break down bile so your liver can reabsorb and reuse bile acids (Cleveland Clinic).
Train your immune system. Cleveland Clinic says your gut contains up to 80% of your body's immune cells, and helpful microbes help train them. See our guide to how the immune system works for the bigger picture.
Crowd out germs. Helpful microbes compete with harmful ones for space and nutrients (Cleveland Clinic, Harvard).
This is where a lot of online claims run ahead of the science. Harvard says scientists are still in the early stages of understanding the microbiome's broad role in health. Cleveland Clinic says healthcare providers are both optimistic and cautious, and that the more we learn, the more we realize how much is left to learn. Areas still under study include:
The gut-brain connection. Some gut bacteria make or trigger chemical messengers such as serotonin, and researchers are still investigating links to mood and nerve conditions (Cleveland Clinic).
Weight and metabolism. Cleveland Clinic says obesity, insulin resistance and type 2 diabetes have some relationship with certain gut microbes, but exactly what it is is not clear yet.
Environmental effects. NIEHS describes research on how pollution, artificial sweeteners, high-fat diets and chronic stress change the microbiome, but many of these findings come from studies in mice, not people.
New treatments. NCCIH says researchers are exploring links between microbiome changes and diseases and developing ways to modify the microbiome. A fecal transplant is so far approved only for repeated C. difficile infections that resist antibiotics (Cleveland Clinic).
Harvard explains that dietary fiber can only be broken down and fermented by microbes living in your colon. That fermentation makes short-chain fatty acids, which lower the pH of the colon and help limit the growth of some harmful bacteria such as C. difficile. Fibers that feed helpful microbes are sometimes called prebiotics. Harvard lists especially good sources as garlic, onions, leeks, asparagus, Jerusalem artichokes, dandelion greens, bananas and seaweed, and says fruits, vegetables, beans and whole grains such as wheat, oats and barley are all good sources.
Cleveland Clinic says a variety of microbes needs a variety of plant fibers, and that a diet high in sugar and saturated fat tends to favor less helpful microbes.
Go slowly. Harvard warns that adding a lot of fiber suddenly can cause gas and bloating, and that people with irritable bowel syndrome should start with small amounts. Our guide to high-fiber foods has a full list.
Example day (an example only): oats with banana at breakfast, a bean and barley soup with onion and garlic at lunch, an apple as a snack, and a vegetable stir-fry with brown rice at dinner.
Harvard lists fermented foods that may contain live, beneficial microbes: kefir, yogurt with live active cultures, pickled vegetables, tempeh, kombucha, kimchi, miso and sauerkraut. Not every fermented food still has live microbes, though. Heating or pasteurizing after fermentation kills them, as in sourdough bread and heat-treated fermented vegetables. If you want live cultures, look for yogurt labeled with live active cultures.
Probiotics are live microorganisms intended to have a health benefit, found in some foods and in supplements. The National Center for Complementary and Integrative Health (NCCIH) at NIH is cautious:
Much remains to be learned about whether probiotics are helpful and safe for various conditions.
In most cases, researchers still do not know which probiotics help, how much to take, or who would benefit.
Different strains can have different effects. If one kind helps, that does not mean another will.
Probiotics sold as dietary supplements do not need FDA approval before they are sold, and some products have been found to contain microbes not listed on the label.
The risk of harm is greater for people with severe illness or weakened immune systems, and the FDA has warned about serious infections in premature infants given probiotics.
There are promising areas, such as preventing diarrhea linked to antibiotics, but even there NCCIH calls the evidence tentative or moderate. Harvard raises the question of whether a relatively healthy person gains anything from a supplement compared with a fiber-rich diet. NCCIH advises talking to your health care provider before taking a probiotic supplement.
Cleveland Clinic is similarly cautious about home gut microbiome test kits. Healthcare providers generally do not use or recommend them, because we do not yet know enough to turn the results into useful, personal advice.
Antibiotics can wipe out helpful bacteria along with harmful ones (Cleveland Clinic). Take them when prescribed, but do not push for them when you do not need them.
Alcohol and tobacco smoke are listed by Cleveland Clinic among chemicals that can harm the microbiome.
Acid-blocking medicines can affect the microbiome by changing the pH inside your gut (Cleveland Clinic). Do not stop a prescribed medicine without talking to your doctor.
Highly processed foods tend to lack fiber and come with additives (Cleveland Clinic).
The good news, from Cleveland Clinic: your gut microbiome can usually recover from a short exposure, such as a brief course of a medicine you need.
Cleveland Clinic says any digestive symptom that lasts more than a few days, gets worse, or goes away and keeps coming back is a reason to call a healthcare provider. NCCIH adds that you should not use probiotics as a reason to put off seeing your provider about a health problem.
Eat a variety of plant foods with fiber, add fermented foods if you enjoy them, use antibiotics only when needed, and avoid tobacco and too much alcohol (Cleveland Clinic, Harvard).
Not necessarily. NCCIH says it is still unclear which probiotics help and who benefits. Ask your health care provider first, especially if you have a health condition.
Cleveland Clinic says healthcare providers generally do not use or recommend consumer kits yet, because the results cannot give practical, personalized advice.
If you like checking how strong the evidence is behind a health claim, Body Unpacked: Health Atlas is a free education app about food, nutrients and physiology. Its Evidence Lens breaks six common health questions into 23 statements, each labeled by strength of evidence, and its Body Connections Explorer shows the nutrients in 44 everyday foods using USDA data. It works offline with no account, no ads and no analytics.
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Gut Microbiome: What It Is, Function and Health (Cleveland Clinic)
The Microbiome (The Nutrition Source, Harvard T.H. Chan School of Public Health)
Probiotics: Usefulness and Safety (NCCIH, National Institutes of Health)
Microbiome (National Institute of Environmental Health Sciences, NIH)
Digestive System: Function, Organs and Anatomy (Cleveland Clinic)