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Understanding the Gut-Brain Axis

One of naturopathic medicine's key philosophies is that much of what ails us is rooted in the gut, so naturally it is interesting to me that the GI tract has been considered the body’s “second brain”. This is because the GI tract is responsible for not only helping us break our foods down to sustain us with adequate nutrition but also sending signals to other organs and systems such as the brain and central nervous system (CNS) to help regulate our mood and cognitive function.

In the literature, there is a well-established bi-directional path of signals that are sent between the GI tract and the brain which allow the two to communicate with each other. (1,2)

What we eat, how we eat, our genetics, and our microbiome all have an intricate role to play in this process.

If we eat foods that do not agree with us, eat too quickly, eat when we’re stressed, etc. this can result in poor digestion that leads to inflammation in the lining of the GI tract. This inflammation can then lead to a cascade of irritation and immune responses send off a danger signal. One product of this danger signal is the formation of inflammasome complexes. Inflammasomes lead to more inflammation and formation of pores in both the GI lining and blood brain barrier. Both barriers are meant to protect us from invaders from our environment, so you can quickly see how can become problematic.

Ultimately, long standing and profound inflammation can also cause imbalances in the community of beneficial microbes that live in our intestines, which play a key role in how our digestive, immune, hormone, and nervous systems develop & function. In addition to helping us better absorb key nutrients to support mood such as Vitamin B12, zinc, iron and B6, this community can produce chemical messengers that get sent to the brain known as neurotransmitters.

You are probably familiar with different neurotransmitters such as epinephrine which induces excitement or dopamine which promotes a sense of pleasure. Most people don’t know this and it’s quite remarkable that 90% of our happiness hormone serotonin (which supports good mood, sleep, appetite, and libido) is produced in the gut from these microbes.

When we’re thinking about management of Neuropsyciatric concerns such as major depressive disorder, generalized anxiety, bipolar, schizophrenia, and autism you can see how the balance of these flora are an important piece to that picture.

But this is important not just those with neuropsychiatric conditions. The literature also shows that those living with the following have altered communities of microflora compared to a healthy counterpart:

· Neurodegenerative conditions (alzheimers, parkinsons, etc.)

· Autoimmune diseases (multiple sclerosis, etc.)

· Metabolic disorders (type 2 diabetes, PCOS, etc.)

· Skin conditions (eczema, acne, psoriasis, etc.)

· IBS, IBD, constipation, diarrhea, etc.

It is hard to know which is the chicken or the egg in this case, but it is clear that there is an intricate role that these microbes play in the function of these systems, the GI tract, nervous system and immune system.

Fermented foods and probiotics are common recommendations in my practice for this reason. That said, not all probiotics are considered equal and the market can quickly become overwhelming to a new consumer. You will want to speak with a trained health professional to determine which probiotic form, dose, frequency and strains are appropriate for your health needs.


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Disclaimer: this information is meant for educational purposes only and should not be used as a replacement for professional medical advice.



1.) Rutsch A, Kantsjö JB, Ronchi F. The gut-brain axis: how microbiota and host inflammasome influence brain physiology and pathology. Front Immunol. 2020;11.

2.) Bull MJ, Plummer NT. Part 1: the human gut microbiome in health and disease. Integr Med (Encinitas). 2014;13(6):17-22.


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