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Gut Bacteria & Autoimmunity: A Strong Connection

The digestive tract is a major player in autoimmune disease. There are numerous factors within the gut which can individually contribute to the pathogenesis of autoimmune disease. One of those factors is the gut microbiome: the bacteria within our gut.

The gut has various mechanisms to ensure beneficial intestinal microbiota, it stops microbiota overgrowth and restricts pathogenic colonization and growth [1].

A Clear Connection Between Microbiome and Autoimmune Disease

There are countless animal and human models proving the case that the microbiota can influence autoimmune pathology [1].

Animal Models

There are certain aspects of disease we can only test in animal models. For example, we can transfer the gut bacteria from one animal to another and see what happens. In fact, one study did just that; they transferred bacteria from rats with autoimmune thyroiditis into the guts of health rats and found the healthy rats developed autoimmune thyroiditis [1]. This proves the gut bacteria has a profound effect on disease pathology.

Human Studies: A lot of Evidence for Various Conditions

Human studies looking at the guts of patients with various autoimmune diseases show dysbiosis (or imbalanced gut bacteria) plays a crucial role [2].

The following conditions are all known to have very particular changes to gut bacteria; as such, treatments (especially probiotics) need to be unique to the individual and the condition they are dealing with [2].

  • Asthma
  • Eczema (aka Atopic Dermatitis)
  • Fibromyalgia (which some argue has autoimmune etiology)
  • Guillian-Barre Syndrome
  • Inflammatory Bowel Diseases
    • Ulcerative Colitis
    • Crohn’s Disease
  • Multiple Sclerosis
  • Psoriasis
  • Psoriatic Arthritis
  • Systemic Lupus Erythematosus
  • Systemic Sclerosis (Scleroderma)
  • Type 1-Diabetes
  • Vasculitis
  • Vitiligo

How Does the Gut Impact the Immune System?

There are various factors by which the gut bacteria can modulate the immune system. The way they work is by producing and releasing metabolites such as short chain fatty acids and cytokines. These factors will influence several physiological pathways, including inflammation.

Short Chain Fatty Acids: these are produced by fermentation of non-digestible carbohydrates.  They help promote cell growth and modulate the immune cells.

Cytokines: these are a large group of proteins – released by specific cells of the immune system. They work as signalling molecules, meaning they can control and regulate the immune system, inflammation and overall balance of the body.

To Treat Autoimmune Disease, We Must Consider the Gut

When treating any autoimmune disease, we must consider the gut, specifically the gut microbiome (bacteria).

There are various ways we can focus on the gut bacteria:

  1. Dietary change: consuming fermented foods, prebiotic fibers [1][2] and low carb diets may be beneficial
  2. Probiotic Supplements [3]
  3. Possibly prebiotic supplements

If there is evidence of bacterial overgrowth, which may be indicated through specialized testing, we may also need to work on eradicating infection.

Check my site on more of these specific topics listed above.


The microbiome, or the bacteria in our gut, plays a vital role to immune function. Disturbances to gut bacteria are found in various autoimmune diseases. Treating autoimmune disease involves focusing on restoring the gut, and special emphasis needs to be placed on treating the gut.

Book in with a naturopath to get a better understanding on how this can be tailored for you!


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