What is the gut microbiome—and how can it affect your health?

ByChristina Sterbenz

Published June 30, 2023

• 9 min read

Have you ever felt “butterflies” in your stomach when you’re excited or nervous? Or realized you’re suddenly hungry after a pizza commercial comes on TV? Well, that’s your gut communicating with your brain. 

The gut has its own microbiome, a community of microscopic organisms, like bacteria, viruses, fungi, and parasites, that live inside our intestinal tracts. The body has four other major microbiomes, too: respiratory, skin, urogenital, and the mouth. Altogether, they make up the human microbiome, the trillions of microbiota that live inside and on the body. 

Your microbiome is essential to your health. But what exactly is it? Think about it like a miniature ecosystem, says Justin Sonnenburg, a professor of microbiology and immunology at Stanford University’s School of Medicine. 

“A good analogy is thinking about a rainforest—many species of many shapes and sizes coming together, but at the microscopic scale, to make these complex communities with different body sites,” he says. 

(Chronic fatigue syndrome is a puzzle. Your gut microbiome may have the key.)

The importance of these tiny worlds can’t be overstated. They help protect the body against invading pathogens, activate the immune system, and digest food, to name just a few functions. Most gut microbes are helpful, while others are harmful. But even favorable microbiota can cause problems, like a yeast infection or disease, if they’re out of balance.

Of the major microbiomes, the gut is the most studied and thus, understood. Here’s what we know about how it affects your health—and whether it’s possible to influence it.

What is the gut microbiome?

The gut microbiome is made up of all the microbiota that live in our intestinal tracts, including the stomach. Most, however, hang out in the colon, the longest part of the large intestine. 

These minuscule organisms, especially bacteria, help the body break down carbohydrates, proteins, and sugars, into useful nutrients and process fiber in the colon. 

“Everything we eat and drink and we don’t digest and absorb goes down through our intestinal tract to our distal intestine, to our colon, where the majority of the microbes are and becomes food for the microbiome,” says Gail Cresci, a microbiome researcher in the department of pediatric gastroenterology, hepatology, and nutrition with Cleveland Clinic Children’s. 

More complex relationships between gut microbiota and health exist too. Numerous studies have shown that the excess or lack of certain bacteria in the gut have a strong correlation to the onset of diabetes; consuming fiber, for instance, can increase microbiota diversity, reduce blood glucose levels, and help people maintain a healthy weight. 

When the gut microbiome is balanced, however, “the bacteria produce a lot of beneficial molecules and metabolites that are known to be helpful in the body,” Cresci says. For example, vitamin K, known as the “blood clotting vitamin,” is predominantly produced by gut microbes. Folic acid, which helps our body make new cells like skin, hair, and nails, is also made by the gut microbiome. 

(Why do some people love to exercise? It might be their microbiome.)

Everyone’s definition of a “balanced” gut is a little bit different though, which makes it such a complicated part of the body. While a healthy gut has a high level of microbiota diversity, there’s no universal marker of gut health, according to Purna Kashyap, professor of medicine and physiology at the Mayo Clinic. What’s “normal” for someone may not be for someone else. 

The gut-brain superhighway

Another complex element of the gut microbiome is its relationship to the brain, known as the “gut-brain axis.” And there’s a lot of emerging research on the topic. 

The gut provides between 90 and 95 percent of the body’s serotonin, which transmits messages between nerve cells—like the feeling of butterflies—and helps regulate body functions like sleep, mood, and digestion. Gut microbiota also aid in the production of other neurotransmitters and chemicals like dopamine and tryptamine, which play a role in anxiety and depression.

“It’s a total pharmacy in there. It’s like we have a little drug factory in our guts,” Sonnenburg says. “There’s hundreds, probably thousands, of different drug-like compounds that are being produced by our gut microbes and get absorbed into our circulation.” 

The gut even has its own nervous system, the enteric system, often called the body’s “second brain.” It has many of the same neurotransmitters as the brain, which can help sense pain and activate the immune system. It also moves food through the digestive system. 

“It can function completely independent of the brain, if it needed to,” Kashyap says. “If I were to just cut out your entire intestine and put it on the table, it would still move.” 

The relationship between the gut and the brain has been obvious for much longer than humans have been studying it, Kashyap says—for instance, think about how some people experience diarrhea when they’re nervous or stressed or others become constipated when they’re depressed. 

Now, studies have shown that various neurodegenerative disorders, including autism, Parkinson’s disease, and Alzheimer’s, all have an association with dysbiosis, or an imbalance of the gut microbiota, according to Cresci.  

Researchers, however, are still figuring out exactly how the superhighway between the gut and brain works and if the impacts are causation, or just correlation. For example, we know people with depression or other mood disorders often experience constipation. 

“But does gut dysbiosis cause that or does the mood disorder cause gut dysbiosis? That’s what’s not fully known,” Cresci says. 

Sonnenburg agrees. “We’re still kind of right at the beginning of understanding this,” he says. 

How can you improve your microbiome?

If the gut microbiome is crucial to various aspects of our physical well-being, how can we maintain a healthy one—or re-balance it after the stomach flu or a few too many slices of cake? 

What you consume affects your gut microbiome. For example, your body digests foods that are high in sugar and low in fiber quickly, which doesn’t leave many nutrients behind for gut microbiota to consume, while the sugar that doesn’t get digested can feed pathogenic bacteria. Antibiotics, meanwhile, can kill off good bacteria along with the bad.

But the gut microbiome is resilient and will bounce back relatively quickly if that person resumes a healthy diet or stops taking medications, according to Cresci. 

That also means that only a long-term healthy diet can truly maintain or improve your gut microbiome. Experts recommend eating foods high in fiber, like complex carbohydrates found in grains, vegetables, and legumes. You should also incorporate fermented foods, such as kimchi, kefir, and sauerkraut, which contain their own probiotics—live microorganisms that can increase microbiota diversity in the gut. And keep sugar intake low and combine it with fiber, like eating your fruits instead of drinking them in juice. 

However, the jury is still out on manufactured probiotics, a multi-billion industry often touted as a one-size-fix-all for our various microbiomes. The reality is much more complicated and coaxing the gut to accept a probiotic is difficult.

(Prebiotics, probiotics, postbiotics—what’s the difference?)

“Probiotics in this situation are more of a kid who gets transferred to a brand new high school, but they know nobody. They will get kicked out of that group because all the other microbes in that community are used to each other,” Kashyap explains.

In fact, clinical trials for probiotics as treatment for a majority of diseases have not shown a benefit, according to Kashyap, pointing to the American Gastroenterological Association’s guidelines. 

The probiotics market also has a lot of different types and varying levels of quality. Navigating that can be confusing and overwhelming for a consumer. Probiotics also aren’t considered a drug in the U.S., so most aren’t regulated by the U.S. Food and Drug Administration. 

If you are going to take a prebiotic or probiotic supplement, always check with a doctor first. Some can be harmful for people, like those on immunosuppressive medications, according to Cresci. If you do decide to take supplements, she recommends using an online resource like consumerlab.com, probiotics.com, or the National Institutes of Health website, to research the various types and to see if they’ve been approved by the FDA.

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