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Brain Belly - How diet can heal or harm your brain via the gut-brain axis

You've probably heard the phrases "go with your gut" when advised on how to make a decision, or felt "sick to your stomach" when nervous about something. Ever wonder why brain processes like decision making and anxiety are linguistically represented in our stomach? My guess is you probably haven't dwelled much on this question, BUT for those who have, read on. The brain and the gut are connected well beyond language.

Picture of the brain made up with various fruits and vegetable

Bacteria is Boss

"Gut" is another word for the gastrointestinal tract starting with your mouth, winding through your esophagus, stomach, intestines, and colon, and ending with your anus. It's about 30 feet long! When we think about what the gut does, we think of digestion. But the gut (specifically the bacteria in the gut) plays a critical role in many other bodily functions such as immunity, metabolic processes, removal of poisons and toxins, and even gene expression.

It is estimated that the gut has about 100 trillion microbiota...that's approximately 10 times the amount of cells in the entire human body (1).

Gut bacteria is known as microbiota. It's not only comprised of bacteria, but also fungus, viruses, and other cells. Microbiota are found all along the digestive tract. It is estimated that the gut has about 100 trillion microbiota...that's approximately 10 times the amount of cells in the entire human body (1). The composition of this microbiota is established early in life and is unique to each individual. It is influenced by how you were born, the ease or stress of your birth, the environment in which you were raised, and of course, your nutrition (1, 2). However, because it is established early on, does not mean it stays this way for the rest of your life. It is a dynamic environment that can change dramatically with diet, stress, disease, and illness.

The Microbiota Microphone

There is not only one line of communication from the gut to the brain, there are multiple lines of communication. This bacteria boss wants to be heard! The microbiota of the gut communicate to the brain via neural pathways, hormonal signaling, and immune responses.

Infograph of the HPA axis

Neuronal Signaling

The microbiota of the gut communicate to the brain neurally primarily via two pathways: the vagus nerve (a cranial nerve) and the autonomic nervous system (our fight or flight and rest & digest system). Both of these pathways are bi-directional, meaning the gut can send signals to the brain, and the brain can send signals to the gut. These lines communicate both directly (gut neurons to brain neurons) and indirectly by synthesizing neurotransmitters such as dopamine (pleasure/reward), GABA (controller of neuronal activity), and serotonin (mood stabilizer), to name a few. In fact, 90-95% of our serotonin is produced in the gut (2). Because of this, a lot of psychology research is looking at the effect of diet and nutrition on mood disorders.

Hormonal Signaling

The gut and the brain also communicate with each other via the hypothalamic-pituitary-adrenal (HPA) axis originating in the brain. The HPA axis is responsible for our body's management of stress. When stress, or a disruption to homeostasis, is sensed anywhere in the body, the HPA axis is activated and cortisol is released. The point at which one's HPA axis is activated is termed the set point. It is the threshold for when your fight-flight stress alarm goes off. This set point is unique to each person and depends on multiple physical and psychological factors, such as history of chronic pain, depression/anxiety, and... gut health. Animal models have shown that germ free mice, or mice without microbiota, have a lower HPA axis set point, meaning their stress response is activated more easily. When probiotics are introduced to these same mice, their HPA axis set point, and thus their body's response to stress, is normalized (1, 3).

Immune Signaling

The gut has the largest concentration of immune cells in the body that are in constant communication with microbiota, both directly through physical contact, and indirectly through secretion of molecules through the gut lining (3). A key purpose of this communication is for the gut microbiota to signal to immune cells when a harmful pathogen is present and to launch an immune response. Microglia cells in the brain are responsible for launching this immune response when there is infection (like meningitis) or trauma (as in a concussion). Animal studies have show that these brain microglia fail to properly develop and diversify in germ free or antibiotic-treated mice (or mice without diverse microbiota), and even more interestingly, show that these effects can be reversed after 6-weeks of recolonization of gut microbiota (3).

The gut-brain axis: It's a 2-way street

Research has shown multiple genetic, environmental, and situational factors that influence the gut-brain axis (in blue) (3). In turn, the gut-brain axis influences many physical, cognitive, social, and emotional aspects of our lives (in red) (3). Expand each topic below to learn more.

Infograph of hoe the gut influenced the brain and how the brain influences the gut
Cryan JF, O’Riordan KJ, Cowan CSM, et al. 2019

How behavior and environment affect our gut-brain axis


Diet seems like the most obvious impact on the gut-brain axis and that's because it is one of the most influential factors on gut microbiota. Western diets rich in sugar, salt, and fat have been shown to contribute to metabolic disorders (i.e. diabetes), obesity, and systemic inflammation (3). Animal studies have shown that even artificial sweeteners negatively impact gut microbiota (2). A mediterranean diet is considered rich in anti-inflammatories and research has shown it to reduce the incidence of neurological disease, cardiovascular disease, depression, and cancer (3). Ketogenic diets have been show to not only reduce the progression of neurological diseases, but also have a neuroprotective function, reducing symptoms of neurological conditions such as Alzheimer's and Parkinson's (3). It is also noted that consuming 4-6 servings of fermented foods like kimchi, kefir, or sauerkraut, throughout your day significantly increases gut microbiota diversity (2).

Genetics and Epigenetics

Mode of delivery




How our gut-brain axis affects our behavior

Food intake

Two mechanisms by which gut microbiota influence food intake are cravings and sensitivity to taste. One proposition is that the more microbiota diversity in your gut, the more competition among microbes. Because of this competitive environment, your gut signals to your brain to seek out, or crave, nutrients which support a particular microbe, thereby maintaining healthy gut microbiota diversity. The less microbiota diversity, the less competition, and thus less craving for nutritionally rich foods. In addition to this, multiple studies have shown that microbiota influence one's sensitivity to taste. Obesity, for example, has been associated with decreased sensitivity to sweet and fatty tastes, thus requiring more intensely sweet or fatty foods in order to perceive that taste (3).



Social Interaction


"You are what you eat."

It's no wonder our language has developed multiple idioms and expressions linking the gut to our brain and behavior. And while research has made huge strides in verifying this connection, we still have a lot to learn about the intricacies of the gut-brain relationship. While I am not a nutritionist or dietician, I always ask my patients about their diet. I often encourage many of my patients with chronic post-concussive symptoms, to consult their doctors, naturopaths, or dietitians for recommendations on anti-inflammatory diets that can assist in managing their symptoms. Sometimes, the smallest changes in diet can have huge impacts on brain health and healing.


  1. Wang HX, Wang YP. Gut Microbiota-brain Axis. Chin Med J (Engl). 2016;129(19):2373-2380.

  2. Huberman A. Huberman Lab. How to Enhance Your Gut Microbiome for Brain & Overall Health. 2022. Accessed April 23, 2022.

  3. Cryan JF, O’Riordan KJ, Cowan CSM, et al. The Microbiota-Gut-Brain Axis. Physiological Reviews. 2019;99(4):1877-2013.


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