Understand Your Gut Microbiome and How to Keep It Healthy

It’s been a long day on the go, and so you grab a burger and fries from the drive-thru. Within hours, your stomach hurts and you feel bad overall. That’s because fatty and highly processed foods are damaging to your gut microbiome, and your gut has a huge effect on your health.

“Gut health needs to be protected,” says Andrea Azcarate-Peril, PhD, professor of medicine at the UNC School of Medicine and director of the UNC Microbiome Core. “We don’t think enough about what we put in our body, and the most important way to support the gut microbiome is by making consistently healthy dietary choices.”

Dr. Azcarate-Peril explains what the gut microbiome is and how you can improve your gut health.

What is the gut microbiome?

The gut microbiome is a collection of trillions of microorganisms in the intestinal tract, including bacteria, yeast, viruses and fungi. Every person has a unique microbiome, and the specific makeup can change depending on your food, your medications and your environment. Many of these microorganisms within the gut are considered healthy or beneficial, while others have the potential to cause harm if they aren’t kept in check by the beneficial ones. The microbes within the gut microbiome play an important role in overall health.

“The traditional understanding of the gut microbiome’s effect on health relates to its role in digestion,” Dr. Azcarate-Peril says. “The bacteria break down fiber and starches that we can’t digest on our own, and they produce short-chain fatty acids that improve gut health. They also help us absorb certain vitamins.”

In recent decades, research has shown that the microbiome’s influence reaches far beyond the gut.

“We now know more about the gut microbiome’s effect on the immune system and how the microbes prevent pathogens from invading and causing infection,” Dr. Azcarate-Peril says. “Additionally, there is more understanding of the link between the brain and the gut.”

The gut is often called the “second brain” because conditions such as stress, anxiety and depression may be linked with signals transmitted by organisms within the microbiome.

Dr. Azcarate-Peril says that more bodily functions might be shown to have a link with the gut microbiome.

“The gut microbiome has a systemic effect on health, but how clear those effects are will depend on the person and their overall health,” she says. “If a person has a headache, it’s possible there’s a link to the gut microbiome; it’s also possible they just didn’t drink enough water that day.”

What happens when there is an imbalance in the gut microbiome?

If you’re generally healthy and your bowel movements are regular, then your gut microbiome is likely well-populated with beneficial bacteria that support bodily functions. Dysbiosis refers to an imbalance that can occur in the gut microbiome when there aren’t enough beneficial bacteria or there is an increase in harmful bacteria.

“How you feel will depend on the extent of dysbiosis,” Dr. Azcarate-Peril says. “Even within a generally healthy microbiome, there can be some minor effects, like a stomachache, bloating, constipation and diarrhea. Then there are major problems associated with dysbiosis, such as inflammatory bowel disease, irritable bowel syndrome and celiac disease.”

Several companies offer at-home microbiome testing kits, in which a person mails a stool sample to a lab, but Dr. Azcarate-Peril advises caution.

“If you send the same sample to five different places, you’ll likely get five different results,” she says. “Those tests are very subjective, and your results will depend on the time of day you obtained the sample, what you ate that day, what method the lab uses and how they interpret the results.”

Instead, you may want to ask whether recurring or persisting symptoms could be related to an imbalance in your gut microbiome, Dr. Azcarate-Peril says. A doctor might suggest an elimination diet or a supplement that could help.

In the meantime, Dr. Azcarate-Peril recommends that you keep track of the foods you eat as well as the intensity and frequency of symptoms you feel afterward.

“If you feel poorly after you eat every once in a while, that’s different from feeling poorly every time you eat something, and both of those are different from something like a salmonella infection, when you might need to go to the doctor,” she says.

How can I keep my gut microbiome healthy?

A healthy diet is key to a healthy gut microbiome. What you eat affects which microbes flourish, and healthy food is associated with growth of beneficial bacteria, while fatty and sugary foods are associated with diminished beneficial bacteria.

“The simple answer is to learn how to cook healthy, real food,” Dr. Azcarate-Peril says. “Avoid fast food, ultraprocessed food, preservatives and dyes, which aren’t good for you, and seek out probiotics and prebiotics.”

Probiotics are live bacteria that can help your existing beneficial bacteria. Fermented foods such as yogurt, kimchi, sauerkraut and kombucha are a few food sources of probiotics. Probiotics also can be consumed in supplement form, though Dr. Azcarate-Peril says it’s important to be mindful that these supplements aren’t subject to regulation or oversight.

“If you see a product advertising billions of probiotics, there’s no way to know if that’s true,” she says. “If you see a supplement claiming to make your life perfect, that’s a red flag.”

Prebiotics provide the fuel for probiotics and other beneficial bacteria. Prebiotic foods are high in the types of fiber that can only be digested by beneficial bacteria.

“Prebiotics are a substance the beneficial bacteria can use that we don’t otherwise make in the body,” Dr. Azcarate-Peril says. “Breaking down the prebiotics causes an increase in the number of beneficial bacteria.”

Many fruits, vegetables, beans and whole grains are good sources of prebiotics, but they still need to be prepared healthfully. Adding sugar or fat can counteract the food’s benefits.

If you want to learn more about making healthy food choices for a healthier gut, talk to your doctor. Need a doctor? Find one near you.