Autoimmune Disease and Gut Health

Many people are surprised to learn that gut health plays an important role in immunity, affecting everything from our ability to fight off infections to modulating the immune system and preventing autoimmune disease. After all, the gut microbiota — the collection of microorganisms in the gastrointestinal (GI) tract — plays a vital role in training the immune system so it knows how to differentiate between helpful and harmful microbes.

The gut microbiota is home to trillions of microorganisms such as bacteria, fungi, archaea, viruses, and protists. Many of these microbes are symbiotic — meaning they’re beneficial to the gut microbiota and the human body — while others are pathogenic. This means they have the potential to promote disease: autoimmune diseases included. 

Let’s take a closer look at how gut health affects immunity and how the microbes in your gut can play a role in the development of autoimmune diseases like Hashimoto’s thyroiditis, celiac disease, and lupus. 

Why gut health matters

In a eubiotic (or healthy) gut microbiota, symbiotic and pathogenic microorganisms can typically coexist in the body without issue. The beneficial microbes in the gut (like Lactobacillus and Bifidobacterium) help to keep the harmful microbes in check (like Clostridium difficile, Salmonella, and Helicobacter pylori).

However, this isn’t always the case. Issues can arise when there’s a decrease in microbial diversity in the gut or there are more harmful microbes in the GI tract than beneficial ones. This is known as gut dysbiosis: an imbalance in the community of microorganisms within the gut microbiota. 

Potential causes of dysbiosis include:

• Chronic inflammation in the body.
• Genetics.
• Infections.
• Antibiotic therapy and other pharmaceuticals. 
• Environmental factors (e.g. diet, lifestyle, and additives in foods).

Small intestinal bacterial overgrowth (SIBO) is one type of bacterial dysbiosis, while small intestinal fungal overgrowth (SIFO) is a type of fungal dysbiosis. Dysbiosis occurs in other parts of the GI tract as well — not just the small intestine but also the colon, stomach, and rectum. Dysbiosis can also develop in other parts of the body such as the skin, urinary tract, and mouth. 

When gut dysbiosis occurs, it increases the risk of developing intestinal permeability (or leaky gut): one of the three main triggers for autoimmune disease (along with genetics and environmental factors). Increased intestinal permeability is shown to precede autoimmune diseases in most cases, and both intestinal dysbiosis and leaky gut are associated with autoimmunity as well as other chronic conditions such as obesity, neurodegeneration, non-alcoholic fatty liver disease, and cardiovascular disease. 

Hashimoto’s, gut bacteria, and molecular mimicry

To briefly demonstrate the link between gut bacteria and autoimmune disease, let’s look at Helicobacter pylori (H. pylori): a common bacterium that has been linked to both gut dysbiosis and Hashimoto’s disease. 

One study found that long-lasting H. pylori infection was significantly associated with an increased risk of Hashimoto’s autoimmune thyroiditis among women, noting that H. pylori infection may “trigger an autoimmune response via molecular mimicry” (Dore et al., 2023). In the case of Hashimoto’s, this means the infection (H. pylori) looks similar to our own cells and tissues (the thyroid gland) — causing the immune system to attack the infection as well as the thyroid gland. 

Other infectious agents that may trigger autoimmunity through molecular mimicry include viruses like Epstein-Barr virus (EBV), Cytomegalovirus (CMV), and Parvovirus B19 (PB19); bacteria like Streptococcus pyogenes, Chlamydia trachomatis, and Campylobacter jejuni; and parasites such as Trypanosoma cruzi.

Gut bacteria and autoimmune disease

So how do our gut bacteria play a role in autoimmunity, exactly? Much of it comes down to the integrity of the intestinal barrier and the gut microbiota’s influence on the immune system. 

Since the gut microbiota regulates host immunity, increased intestinal permeability (leaky gut) disrupts the immune system’s ability to regulate itself. When this happens, exterior antigens from the gut can sneak through the intestinal barrier and enter the bloodstream — triggering local and systemic immune responses. If the other two triggers for autoimmunity are in place, autoimmune diseases can also develop.

For example, someone might develop Hashimoto’s autoimmune thyroiditis if they have increased intestinal permeability; have one or more genes associated with Hashimoto’s; and have been exposed to triggers such as radiation to the thyroid gland, environmental toxicants, and iodine deficiency or excess. 

That said, an individual typically won’t develop Hashimoto’s autoimmune thyroiditis unless they have a genetic predisposition to Hashimoto’s disease — even if they’ve been exposed to environmental triggers and have increased intestinal permeability. Depending on their genes; however, they may develop a different type of autoimmune disease (such as lupus, celiac, or inflammatory bowel disease). The bottom line is that all three triggers for autoimmunity need to be present for autoimmune diseases to develop.