What is the gut microbiome?
The gut microbiome is the community of microbes that live in your gut. This includes bacteria, fungi, and viruses.
When people hear words like “bacteria” or “virus,” they often think of getting sick. But the microbes in your gut are not something to fear — they are normal residents of a healthy digestive system.
Your body and your gut microbes work together. The microbes benefit from the food you eat, and in return, they help keep your gut and immune system healthy.
How does my gut microbiome affect my overall health?
Your gut provides the food and environment your gut microbes need to thrive. In turn, your gut microbes help digest parts of food your body cannot break down on its own.
In the process, they produce helpful byproducts that:
- Keep the lining of your gut healthy.
- Support your immune system.
- Help your digestive system run smoothly.
In short, a healthy gut microbiome helps create an internal environment that supports your overall health.
How can I take care of my gut microbiome?
Healthy habits that are good for your body are also good for your gut microbiome.
Gut microbes depend on you for their food — specifically, on the parts of food you cannot fully digest yourself, such as fiber. If you only eat foods that your body fully digests, your gut microbes will have little left to feed on.
A high-fiber, plant-based diet, such as a Mediterranean-style diet, can support a diverse and resilient gut microbiome.
Eat many different kinds of fiber-rich foods
Fiber is the part of plants that your body cannot fully digest. A helpful goal is to eat a wide variety of plant-based foods over the course of a week. Many people aim for around 30 different types. Good sources include:
- Fruits and vegetables – a wide variety is best.
- Beans and lentils
- Whole grains
- Nuts and seeds
- Herbs and spices
Eating a wide variety of plant foods — not just a large quantity of fiber — is what helps build a varied and strong gut microbiome.
As you increase your fiber intake, you may experience abdominal discomfort, bloating, and gas. To prevent or lessen these symptoms, gradually add more fiber to your diet rather than increasing your intake all at once. A helpful approach is to:
- Increase fiber intake by a small amount. For example, about 3 grams per week.
- Maintain that level for 7 to 10 days before increasing again.
- Drink enough fluid to stay hydrated as you add more fiber.
Stay active
Physical activity helps keep things moving through your gut and can help keep bowel movements regular. It is also associated with a more diverse gut microbiome, though the exact amount needed is not known.
General activity guidelines suggest aiming for regular movement most days of the week. You do not need a specific routine or type of activity. Walking, running, cycling, dancing, or any regular movement can support your gut microbiome.
There is no established “dose” of exercise for the microbiome, but regular physical activity is consistently associated with greater gut microbiome diversity and greater “beneficial” organisms. Overall, some activity is better than none.
Drink plenty of water
Staying hydrated can help you maintain regular bowel movements. This helps your gut function properly, which in turn supports a healthy microbiome.
What about probiotics and prebiotics?
Probiotics are live bacteria that are thought to be good for your health. They are sometimes known as “good bacteria.” You can find them in some supplements and in foods like yogurt.
It was once assumed that probiotics could simply crowd out the “bad” bacteria and make your microbiome healthier, but this isn’t always the case. Their effect depends on the specific strain and the condition being treated, and they do not help everyone with digestive problems. If you think probiotics are helping you, talk to your healthcare team about whether you should continue taking them.
Prebiotics are not live bacteria. Instead, they are a type of fiber that feeds the bacteria in your gut. Think of prebiotics as food that helps your gut microbes grow and thrive. Some research suggests that prebiotics may help with certain health conditions, but scientists are still learning about their benefits.
Should I eat fermented foods?
Some fermented foods contain live microbes, including bacteria and yeasts. Examples include sauerkraut, kefir (a tangy milk drink), kimchi (fermented Korean vegetables), and kombucha (a fizzy tea). Some people eat these foods regularly as part of their culture. If you enjoy them, it’s fine to include them in your diet.
Some research, including a clinical trial suggesting fermented foods might increase microbiome diversity, is encouraging. But the overall evidence is still limited, so they are not yet recommended specifically to “improve” your gut microbiome.
How do antibiotics affect my gut microbiome?
Antibiotics can be life-saving and important when you have a bacterial infection — you should not hesitate to take antibiotics your healthcare provider has prescribed to treat it. At the same time, it is helpful to understand that antibiotics can also affect the healthy microbes living in your gut as a side effect, even though they are not the target of treatment.
In most people, gut microbes repopulate, and the gut microbiome returns to a state close to its original state. In a smaller number of people, antibiotics can create an opening for harmful bacteria, such as C. difficile, to take hold, which can cause diarrhea and illness.
Remember
Antibiotics save lives. When you need them, take them as directed.
You can support your gut health by eating fiber-rich foods, drinking water, staying active, and following your provider's advice.
Talk to your health care team
Talk to your health care provider if you have questions about how to support your:
- Digestive health.
- Diet and nutrition needs
- Gut microbiome
A gastroenterologist or registered dietitian can help you build a plan that fits your health needs and lifestyle.
Content adapted from an interview with:
Purna Kashyap, M.B.B.S.
Chair of the AGA Center for Gut Microbiome Research & Education Scientific Advisory Board
Reviewed by:
Jessica D. Korman, MD
Capital Digestive Care, Washington, DC
AGA Patient Education Advisor
September 2026