Repair the Gut-Brain Axis For Autoimmune Health & Happiness

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First, heal the gut.

Minding the microbiome, as you may have gathered from reading this website, is a key therapeutic option for people with autoimmune disorders.  We know that the health of the GI tract (combined with genetics and environmental triggers) is a pivotal factor in the development of autoimmune disorders, although this is still under-acknowledged and under-addressed in mainstream medicine.

If we take it a step further, we can explore how gut and brain health are related and even connect the dots between autoimmunity, inflammation and depression, and even some or all of the autoimmune super symptoms.  Gut health, as well as how the health of the gut and the brain are interrelated, is now thought to be a major factor in depression, anxiety and mood disorders.

Since we know the role that compromised gut barrier function (leaky gut) plays in autoimmunity, it makes sense for Autoimmune Moms to wonder what role the gut-brain axis plays in autoimmune disorders, and more importantly, what role it is playing in our own lives and how we can influence it to accelerate our healing journeys.

For the sake of a general definition, according to Wikipedia, “the gut–brain axis refers to the biochemical signaling taking place between the gastrointestinal tract and the nervous system, often involving intestinal microbiota, which have been shown to play an important role in healthy brain function. “ In other words, the gut-brain axis describes how the gut and brain communicate back and forth, and how the health of each impacts the other.

When there is inflammation in the gut, say when the delicate balance of commensal (good) and pathogenic (potentially harmful) microbes is compromised, inflammatory signaling molecules called cytokines are sent to the brain by immune tissue in the gut.

In fact, while most immune responses produce their initial effects in the peripheral body, information regarding immune challenges are almost immediately signaled to the brain in a sensory-like fashion, meaning an immediate inflammatory impact on the brain resulting from to an immune challenge in the gut to substances like proteins from food or to chemical compounds, such as BPA from plastics.

When the gut is under stress from infection or loss of ecological balance as mentioned above, there is an effort to restore balance by reducing the available stores of tryptophan (the amino acid pre-cursor to the feel-good neurotransmitter, Serotonin) being ingested as food by the pathogenic bacteria.  To accomplish this, the body activates the enzyme indolamine 2-3 dioxygenase, which degrades serotonin and tryptophan, limiting nourishment for bacteria, but potentially contributing to depression and anxiety for us, as well as disturbances in cognition, memory (think brain fog), appetite, sleep and body temperature disturbances (think cold extremities or fevers).

On the flip side, psychological and emotional stress can upset the balance of gut microbes and therefore, induce inflammation in both gut and brain.  This is why stress management through mind-body practices is foundational to any anti-inflammatory or gut-healing treatment plan.  If this aspect of our lives is not addressed, we cannot expect healing to last or, even to take place at all, especially for those who lead high-stress lifestyle or have a history of early emotional trauma.

While depression is not named as an autoimmune super symptom, perhaps it should be.

In one study of 88 patients, which aimed specifically to determine the frequency of depression in patients with systemic autoimmune diseases (SAD), as well as to determine the frequency of pain, fatigue and sleep disorders (again, think super symptoms) in these patients and their relation with depression, depression in patients with systemic autoimmune diseases was shown to be a whopping 69%.

Pain was found in 97% of the depressed patients and in 62% of non-depressed patients.  Sleep disorders were found in 95% of depressed patients and in 60% of non-depressed patients.  Fatigue was found among 80% of depressed patients and 44% of non-depressed patients. [Source]

Wouldn’t it be interesting if the authors had taken stool samples and analyzed patients’ gut microbial populations?  Could it be that the depressed patients had more severe gut inflammation and microbial imbalance?

Even better, it would be wonderful to see a study takes the next step and measures the effectiveness of a Functional Medicine 5-R Gut Restoration Program in depressed and non-depressed patients with systemic autoimmune diseases.  Clearly, there is much research to be done to validate the 5-R approach to mending the gut and optimizing the gut-brain axis in systemic autoimmune disease.  The research that has been done to confirm that disrupted gut health is involved in the initiation and perpetuation of autoimmunity and systemic inflammation, combined with common sense and the collective clinical experience of thousands of Functional Medicine practitioners and their patients, confirms the basis of what ancient forms of medicine like Traditional Chinese Medicine and Ayurveda, and even early medical scholars like Hippocrates, “The Father of Medicine”, have said all along—first heal the gut.

Based on the available evidence, optimizing the gut-brain axis and inflammatory status by restoring and maintaining the balance of the microbiome with Functional Medicine Nutrition as well as Mind-Body Medicine, seems like a valid treatment option for Autoimmune Moms to thoroughly explore.

Our happiness may very well depend on our doing so.


About the Author

Angie King-Nosseir MS, RD is an Integrative and Functional Registered Dietitian, with a passion for walking with people along their path toward health transformation. Angie has a Master’s degree in Nutrition, is a Certified LEAP Therapist, corporate wellness health coach, freelance nutrition and wellness writer, and certified yoga instructor. She is trained in Functional Nutrition and Medicine through the Institute for Functional Medicine and in Food as Medicine through the Center for Mind-Body Medicine.

This post contains opinions of the author. is not a medical practice and does not provide medical advice, diagnosis, or treatment.  It is your responsibility to seek diagnosis, treatment, and advice from qualified providers based on your condition and particular circumstances.  Camino Real Ventures, Inc., the company that makes available to you, does not endorse nor recommend any products, practices, treatment methods, tests, physicians, service providers, procedures, clinical trials, opinions or information available on this website.  Your use of the website is subject to our Terms of Use and Privacy Policy



  1. Dear MS patients,
    I am doing a research project on this subject.
    If any of you have had pin worms before getting an
    MS diagnosis please email me and tell me how long
    did you have that condition before you had your first
    episode with MS.

  2. As a woman who suffers from Graves and the compound heterozygous mutation, this article really resonates. I have been struggling with leaky gut for years. My doctor finally recommended the Physician’s Elemental Diet. I broke down and bought a two day supple for $75, an actual discount. Most sites have it for $47 for a one day supply. He recommended that I do it for a couple weeks, then said at least try it for a day. He agrees the price is steep. I haven’t tried it yet as I want to make sure I have no where to go. I have to see how my body reacts. Wish me luck.

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