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How Your Gut Bacteria Alter Your Thinking

You'd be surprised how much these little bugs can do!

By Austin Perlmutter, MD



  • Our gut influences our brain by way of the gut-brain connection. The gut microbiome is a big part of this story.

  • Gut bacteria impact the immune system (which is linked to our brain state) as well as change levels of molecules like short-chain fatty acids and neurotransmitters

  • Food is one of the biggest ways by which our choices influence the gut microbiome-brain connection

A growing body of evidence suggests that what happens in our gut can influence our cognition, which means it alters the way we think. Specifically, the gut microbiome (the trillions of microbes living in our GI tract) are thought to connect to and influence brain function through the gut-brain axis (the two-way connection between gut and brain). Here are just a few of the interesting ways in which the gut microbiome may impact our thoughts!

The gut microbiome generates a range of molecules that may impact brain function

The gut microbiome is tremendously active, both in breaking down molecules and creating new ones. In fact, it the bacteria in our gut produce and metabolize a wide range of molecules that may either directly or indirectly affect our brain function. A good example is that our gut microbes can produce short-chain fatty acids (SCFAs), tiny fats that (mostly in pre-clinical research) are linked to improvements in cognition for certain populations. Gut microbes can also synthesize amino acids and vitamins that are key to a variety of brain processes. However, it’s still unclear to what extent the nutrients created by the gut microbiome are actually bioavailable to the brain.

The gut microbiome may alter cognition through the immune system

The gut microbiome also speaks to and may influence the brain by way of the immune system. Alterations in immunity (specifically elevation in chronic inflammation) are linked to increased risk for developing worse cognitive function including risk for Alzheimer’s dementia. Very high spikes in inflammation (as are sometimes seen in critically ill patients) are linked to delirium, a state of confusion and generally altered mental status. Since the gut microbiome directly communicates with and influences immune cells (which are mostly located in the gut), the link between immunity, cognition and the gut microbiome is certainly worth knowing.

How about the link between food, the gut microbiome and cognition?

With trillions of individual bacteria that are being affected each day by our dietary choices, the gut microbiome is very responsive to our diet. Consuming the standard American diet (or “Western diet”) which is rich in processed foods, less-healthy fats and added sugars is thought to contribute to a less healthy microbiome. It’s also been linked to an increased risk for developing Alzheimer’s disease. Having a less healthy makeup of the gut microbiome with more species that produce inflammatory molecules (which seems to happen as we age, as well as with an unhealthy lifestyle) has itself been linked to Alzheimer’s disease. These are a few of the reasons why so many health experts recommend a diet filled with a diversity of colorful fruits, vegetables, and other forms of fiber that are linked to better health of the gut microbiome.

Take away message:

To summarize this somewhat complex science, the gut microbiome may act on our brains and change our cognitive state through a variety of pathways, but the immune (which includes inflammation) and metabolic (including short-chain fatty acids) pathways may be two of the most important.

This science furthers the idea that choosing a lifestyle the health of our gut microbiome may represent a long-term investment in our brain health. For information on how to foster an overall healthier gut-brain connection, including a healthier gut microbiome, this article offers a number of practical tips. Look out for future articles to learn how the gut microbiome changes our mood and our behavior!

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A version of this article I wrote was also published on

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