Gut Feelings: How the Creatures in Your GI Tract Talk to Your Brain

Have you ever had that feeling of something not being quite right, despite not being able to put your finger on it? This sense of intuition is also known as your “gut feeling,” and for good reason. Recently, the gastrointestinal (GI) tract, including your stomach and intestines, has been referred to as the “second brain” in the body.[1] There’s a secret little world in your GI tract that makes it so smart. Let’s explore it!

There are millions of colonies of bacteria, viruses, and fungi living in and on your body, including your digestive tract.

CDC/Bacteroides biacutis/Public Domain

The mix of bacteria, fungi, and viruses in and on us is known as the microbiome, and scientists are now starting to pay attention to how our diets, hygiene practices, and genetics affect it – and, in turn, what it does for our health. These organisms help break up foods that our bodies would be unable to digest on their own. The amounts of and types bacteria in your gut are different from anyone else’s, thus making it your internal fingerprint.[2] While your daily activities affect your microbiome, the same is true in reverse. An unbalanced ratio of certain bacteria may be related to poor health, including conditions like allergies, celiac disease, gastric cancer, autism, obesity, anorexia, irritable bowel disease, and type 2 diabetes.[2] However, your microbiome affects more than just the immune or digestive system. One recent discovery is that there may be a connection between the bacteria in your GI tract and your brain.

Gut microbes talk back to the brain, affecting mood and behavior

Animal studies have shown a relationship between the brain and gut organisms. In one experiment from 2010, mice that did not have any bacteria in their gastrointestinal tracts showed less anxiety than mice with standard amounts of gut bacteria.[2] In another study, rats who were subjected to stress early in life had altered gut microbiomes, as well as more disorders of bowel function, compared to animals not who did not experience early stress.[3]

In studies on humans, it was found that there is an association between gut health and mental health, and disorders such as irritable bowel disease have been associated with anxiety.[4] Additionally, depression has been thought to be due in part to nutritional deprivation, possibly linked to bacterial overgrowth in the small intestine. Along with the bacterial overgrowth contributing to depression, stress has been found to lower levels of two other naturally occuring bacteria in the gut, lactobacilli and bifidobacterium.[5]

So, what does this mean for you? What is the ideal balance of bacteria in the gut, and how do you achieve it? Some things that affect your microbiome are out of your control, such as your genetics. However, healthy behaviors, like eating high-fiber meals (think fruits, vegetables, and whole grains) and exercise, are good for the friends in your gut. And when you benefit your microbiome, your brain may benefit too.

Jon Sullivan/Still Life of Fruits and Vegetables/Public Domain


  1. M. Avetisyan, E. M. Schill, R. O. Heuckeroth, Building a second brain in the bowel. J. Clin. Invest. 125, 899–907 (2015). doi:10.1172/JCI76307pmid:25664848
  2. Cryan, J. F., and S. M. O’Mahony. “The microbiome-Gut-Brain axis: from bowel to behavior.” Neurogastroenterology & Motility, vol. 23, no. 3, Aug. 2011, pp. 187–192., doi:10.1111/j.1365-2982.2010.01664.x.
  3. Clemente J, Ursell L, Parfrey L, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell. 2012. Accessed February 2018.
  4. Neufeld KM, Kang N, Bienenstock J, Foster JA. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol Motil 2010; 23: 255–64.
  5. O’Mahony SM, Marchesi JR, Scully P et al. Early life stress alters behavior, immunity, and microbiota in rats: implications for irritable bowel syndrome and psychiatric illnesses. Biol Psychiatry 2009; 65: 263–7.
  6. Logan AC, Katzman M. Major depressive disorder: probiotics may be an adjuvant therapy. Med Hypotheses 2005; 64: 533–8.

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