The Brain-Gut Connection, Explained

Your brain and your gut are in constant contact, and together they play a big role in your mood, thinking and memory

Christine Richmond

Updated June 03, 2025

A female doctor showing a male patient a tablet with an image of a brain from an MRI scan

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Every day, your gut and brain talk to each other. They send signals back and forth relaying information about your appetite, stress levels and more. This crosstalk is the reason why a stressful situation like giving a speech might trigger a feeling of “butterflies” in your stomach. It also helps explain why people with irritable bowel syndrome, or IBS, are prone to anxiety, and why many drugs used to treat mental health issues, such as SSRI antidepressants, can come with gastrointestinal side effects.

The brain-gut connection can affect your mood and behavior and, later in life, your cognitive function, research suggests.

So what exactly is happening inside your body when your brain and gut communicate? It’s a complex interplay that also involves your endocrine and immune systems. But these are the key players:

Enteric nervous system

What it is: A vast network of hundreds of millions of neurons, or nerve cells

Where it's found: The entire length of your digestive tract

What it does: Nicknamed the “second brain,” the enteric nervous system is in constant contact with your actual brain. Yet it works independently to manage everything about your digestion, including the muscle contractions that move food through the digestive tract.

Vagus nerve

What it is: One of 12 cranial nerves that link your brain to different parts of your body

Where it's found: It travels from your brainstem to your abdomen

What it does: The vagus nerve is the main pathway by which your enteric nervous system and your brain communicate. Think of it like an ethernet cable connecting your gut and brain, says Hariom Yadav, director of the Center for Microbiome Research at the University of South Florida.

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Gut microbiome

What it is: A complex ecosystem in your gut composed of trillions of microbes, including bacteria, viruses and fungi

Where it's found: Mainly in your colon, the largest part of the large intestine

What it does: The gut microbiome breaks down the complex carbohydrates and fiber that reach your large intestine undigested. This activity creates many important substances, including hormones and certain vitamins. Some of those substances have an indirect influence on the brain-gut connection; others target the brain directly.

Here’s how those key players interact

The gut and brain use two routes to communicate: the vagus nerve and the bloodstream. “If something needs to be sent immediately, it goes through the vagus nerve,” which sends signals back and forth in milliseconds, Yadav explains. This is what’s happening when your stomach is “in knots” right before a big presentation.

The brain and gut also interact through products of the microbiome that travel through the bloodstream, although this can be a slower process, he adds. For example, gut microbes trigger the production of small molecules that enter the bloodstream and travel to the brain. Once there, the molecules affect the function of immune cells in the brain called microglia, which are involved in inflammation, tissue repair and cognitive function. This can be good or bad. Scientists are studying whether variations in microbiome composition, for instance, may help to either reduce Alzheimer’s disease risk or speed up progression of the disease, according to Rob Knight, a co-principal investigator at the Alzheimer Gut Microbiome Project.

Gut microbes also make short chain fatty acids (SCFAs) as they feed on fiber. Moving through the blood stream, those SCFAs regulate metabolism and support brain health by producing substances such as serotonin, a neurotransmitter and hormone that helps to regulate mood, learning, sleep and more. “In fact, 90 percent of your body’s serotonin is made in the gut,” Yadav says.

How you can keep the conversation healthy

Because your brain and gut are linked, a disruption in one can cause a disruption in the other. An unhealthy gut microbiome that has more potentially harmful microbes than beneficial ones and lacks overall diversity is called dysbiosis, and there’s evidence it can increase your risk of chronic disease. Gut microbiome composition and function was found to be different in people with Alzheimer’s disease versus cognitively healthy adults in a study of 232 adults ages 47 to 93, in a preprint that was posted on MedRxiv in 2024.

“You can help keep your microbiome healthy and with a diverse mix of residents by eating a variety of fiber-rich foods and getting regular exercise.”