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How Your Gut Microbes Control Your Mind

3 pathways connecting your gut microbes to your thoughts and mood



  • Microbes in your gut (aka: the gut microbiome) may change the way you think and feel

  • Microbes in the gut may be capable of changing brain function through their effects on the vagus nerve

  • Changes in immune function that affect our brain function may be driven by gut microbes

  • Breakdown products of gut microbes (like short-chain fatty acids) may have a variety of effects on our brain state

In the mid-1880’s, a pediatrician named Theodor Escherich was among the first to propose a controversial idea: bacteria could live within our gut without causing health issues. This concept has exploded in medical and popular conversation since then, with the significance of the “microbiome” (the microbes that live on and in us) gaining traction as a way to understand and even address a number of health concerns.

Differences in our microbiome (especially the one in our gut), have been linked to everything from how long we live to our risk for developing diabetes. But perhaps most interestingly, it’s now shown that these tiny bugs in our GI tract may in fact be altering our thoughts. Here are 3 fascinating ways this could happen.

1. The Vagus Nerve

The gut and brain are thought to be closely connected through the gut-brain axis. This terminology is often expanded now to include the microbiome in what’s been labeled the microbiota-gut-brain axis. When understanding how signals from the gut could reach the brain, many researchers focus on the vagus nerve. As the longest of our cranial nerves, the vagus nerve runs back and forth from the brainstem to the large intestine (as well as a number of other locations in our bodies).

Research is now revealing that what happens in the gut influences our brain by affecting the vagus nerve. And it seems to be the case that our microbiome may directly affect the signals conveyed by the vagus nerve to the brain.

Recent scientific work has shown that the microbes in our gut, as well as their products are able to influence the firing rate of the vagus nerve and therefore the message it’s sending the brain. This message in turn is thought to influence brain function, as well as state of mind. How is this happening? The nerve endings of the vagus nerve in the gut are sensitive to a number of things produced by microbes ranging from SCFAs to neurotransmitters like serotonin, norepinephrine and GABA. These endings are also sensitive to immune signals like inflammation.

In animal studies, it has been shown that signaling from the gut to the brain by way of the vagus nerve is key to the antidepressant effects of selective serotonin reuptake inhibitor (SSRI) drugs, while mood-boosting effects of certain healthy microbes (probiotics) were dependent on the vagus nerve’s function. More recently, it’s been shown that activation of the nerve in humans appears to influence emotional processing, showing a direct connection between state of mind and the vagus nerve.

2. The Immune System

One of the most convincing links between the gut and our mental health relates to the immune system. Far more than a simple defense against germs, our immunity is tasked with carrying out complex signaling throughout our bodies. But most of our immune systems is located in the gut, where it responds in real time to the information presented by the outside world, including the microbiome.

Researchers have shown that the gut microbiome and the immune system are in constant bidirectional communication, influencing each other at every moment. When we understand that the state of our immune system is closely linked to our overall brain and our mental health, the role of our microbiome becomes even more significant. For example, high levels of inflammation are linked to an increased risk for developing depression, and may lead people to make more impulsive decisions.

The state of the gut microbiome is thought to influence immunity in a number of ways, ranging from direct communications between bacteria and immune cells to its effects on the strength of the gut lining (which then influences the state of our gut immune system). It’s also thought that signals from the microbiome may get into the bloodstream, where they can reach the brain and potentially influence the brain’s immune system.

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3. Microbiome metabolites like short-chain fatty acids (SCFAs)

Each day, we consume a dazzling array of different substances. Some of these our bodies can easily break down (for example, carbohydrates in bread are rapidly converted into glucose, which we can quickly absorb through our gut lining). Yet despite our incredible biology, we lack the enzymes to break down a number of dietary components. Luckily, we can get a little help from our microbiome in extracting value from these indigestible molecules.

One of the best examples of microbes assisting with digestion relates to fiber. Our guts can’t absorb or break down fiber in our foods. But when certain bacteria in the gut come into contact with fiber, they digest it and produce molecules called short-chain fatty acids (SCFAs). Unlike fiber, we’re able to make use of SCFAs. And research is demonstrating that one way SCFAs may influence our health is through their effects on our brains and our mental state.

In one 2020 paper, researchers showed that having higher levels of SCFAs in the gut was linked to lower cortisol levels when healthy men were psychologically stressed. It’s also thought that SCFAs may help dampen inflammation, which may then lead to a host of brain benefits that improve mood.

Putting it together:

It’s increasingly clear that what happens “in our heads” is actually a reflection of what happens in our bodies. Despite the physical distance between our GI tract and our brains, it’s now understood that what happens in the gut is affecting a number of pathways in our brains, many of which may be a direct effect of the state of our microbiome. This is all more reason to have empathy for the complicated signals that influence the mental states of others and ourselves, as well as to consider prioritizing our gut and microbiome health as a way of prioritizing our cognitive and mental health.

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A version of this article I wrote was also published on

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This was a great information article. I’m a retired RN but my last 8 years of work was in Integrative/Functional medicine! Even non/medical persons can understand most of your informst if they just read it!

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