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Your Body's Second Brain

Updated: Mar 2, 2022

The Gut Microbiome

The human gastrointesinal tract, which is composed of the esophagus, stomach, small and large intestines, pancreas, gallbladder and liver, contains trillions of microbes known as the gut microbiome, aka, the gut flora. Your unique microbiome is influenced by numerous factors such as genetics, age, sex, diet, environment, and lifestyle. The organisms within your gut have the power to directly impact brain development, mood, behaviour, physiology, metabolic functions and immune system (3). How?

The Enteric Nervous System and Gut-Brain Axis

Have you ever heard of the saying “trust your gut” or “go with your gut”? It turns out there is truth behind these expressions. Embedded within your gastrointestinal tract, there is a network of neurons, neurotransmitters and proteins that are identical to many of those found in the brain. This neural network is known as the enteric nervous system (ENS).

The ENS produces more than 30 neurotransmitters and has more neurons than the spine!! Since the structure, chemical coding and function of the ENS is similar to that of our brain, the ENS is known as a second brain … in our gut! This "second" brain directly impacts your mood and mental health status through the gut-brain axis (GBA), which is the bidirectional connection between the central nervous system (brain and spinal cord) and the enteric nervous system, ultimately linking the brain's emotional and cognitive function with gastrointestinal function (4). I know, mind blowing!

The Gut Microbiome and Mood

The bacteria within our gut microbiome produce neurotransmitters (chemical compounds which directly impact our cognitive functions) such as dopamine (feel-good/ reward hormone), norepinephrine (concentration hormone), epinephrine (fight or flight hormone), serotonin (happy hormone), GABA (calming hormone), acetylcholine (learning neurotransmitter) and glutamate (memory neurotransmitter) (3). In fact, several studies done on germ free mice (mice that have no gut microorganisms residing within them) found that these mice have substantially reduced levels of norepinephrine in the large intestine along with lower levels of serotonin in the blood, when compared to those of controls (3). Additionally, studies conducted on GF animals indicate that the microbiota regulates the hypothalamic-pituitary-adrenal axis (HPA axis), a system which controls the body's stress response and anxious behaviour. The mice without bacteria had an increased stress response as indicated by augmented levels of cortisol (4). These findings support the idea that bacteria within the gut produce neurotransmitters, thereby influencing our mood, as well as mental health.

More specifically for example, members of the Bifidobacterium and Lactobacillus bacteria families have been reported to produce GABA, a neurotransmitter that helps lower anxiety, reduce stress and provide a sense of calmness (3). Consequently, altered GABA production is linked to feelings of anxiety, stress and sleep disturbances(3).

Fun fact: the field of study that investigates gut microorganism's ability to influence behaviour through production of neurochemicals analogous to those produced by the nervous system is called microbial endocrinology. Isn't that cool!

Can the Gut microbiome directly communicate with the CNS?

Apart from indirectly influencing mood through the production of neurotransmitters, the enteric nervous system and Gut Microbiome directly communicate with the brain (and vice versa) through the vagus nerve. This nerve runs from the brain, through the body, all the way to the intestines (7).

If we know that the gut influences our cognitive abilities, it is probably important that our gut functions optimally right? But what is a healthy gut?

Whether your microbiome affects your mental and physical health positively or negatively depends on the unique classes of bacteria which encompass your gut. More specifically, it is dependent on the ratio of symbionts (good bacteria) to pathobionts (bad bacteria). Although no two microbiomes are exactly alike, the composition of the gut flora differs in “healthy” individuals compared to those with illnesses (3). For example, one study (4) showed that the amount of Firmicutes bacteria found in the GI tract of patients with Type 2 Diabetes was lower when compared to non-diabetic persons, while the number of Bacteroides and Proteobacteria was higher. A greater concentration of harmful bacteria in the gut is referred to as dysbiosis, a condition linked to neuropsychological disorders, such as, depression, anxiety, obsessive-compulsive disorder and autism spectrum disorder, as well as, metabolic and gastrointestinal disorders, including obesity, inflammatory bowel disease and irritable bowel syndrome (5).


  1. Government of Canada, S. C. (2015, November 27). Health at a Glance. Mental and substance use disorders in Canada.

  2. Mental Illness and Addiction: Facts and Statistics. CAMH. (n.d.).

  3. Strandwitz P. (2018). Neurotransmitter modulation by the gut microbiota. Brain research, 1693(Pt B), 128–133. Mittal R, Debs LH, Patel AP, Nguyen D, Patel K, O'Connor G, Grati M, Mittal J, Yan

  4. Carabotti, M., Scirocco, A., Maselli, M. A., & Severi, C. (2015). The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Annals of gastroenterology, 28(2), 203–209.

  5. Mittal R, Debs LH, Patel AP, Nguyen D, Patel K, O'Connor G, Grati M, Mittal J, Yan D, Eshraghi AA, Deo SK, Daunert S, Liu XZ. Neurotransmitters: The Critical Modulators Regulating Gut-Brain Axis. J Cell Physiol. 2017 Sep;232(9):2359-2372. doi: 10.1002/jcp.25518. Epub 2017 Apr 10. PMID: 27512962; PMCID: PMC5772764.

66 views2 comments


rahel horvath
rahel horvath
Jun 29, 2021

this was such a great read! easy to understand and digest. I will definitely be paying more attention to which foods I eat to improve my mood!


Such an incredible read!!! Very informative and easy to understand. The topic you wrote about is so interesting and I enjoyed every second of it! Well done and keep up the amazing work.

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