What’s the Relationship Between Gut Health and Autoimmunity?

Medically Reviewed
Key Takeaways

The gut microbiota is a collection of microorganisms that play a vital role in the regulation of many physiological processes, including immunity.

Irregular gut microbiota composition is involved in autoimmunity and specific autoimmune disorders, but it isn’t clear if altered gut microbiota composition causes a disease state, or vice versa.

Changing your diet may help strengthen your gut microbiota and reduce autoimmune disease development or progression. However, more research is needed to establish the clinical efficacy of dietary changes.    

Medically Reviewed By
Dr. Anshul Gupta
Written By
WellTheory Team

The human gastrointestinal (GI) tract plays a vital role in regulating interactions between us, our food, and foreign substances entering our bodies. It is believed there are more than 1014 (that’s 10 followed by 13 zeros!) microorganisms living in the human gut. (Source)

In today’s question and answer, we will explore how gut health, autoimmunity, and autoimmune diseases are related, where digestive issues fit into this relationship, and how your gut–immune system relationship can be strengthened to achieve better health.   

What Is the Gut Microbiota?

The gut microbiota, or microbiome, comprises the wide array of microbes in our small and large intestines, including bacteria, viruses, and yeasts, that have co-evolved with us over thousands of years. 

The gut microbiota provides many benefits to us, their hosts, including regulation of GI functionality, metabolism, immunity, and defense against pathogens. Changes in the gut microbiota, however, are implicated in development of autoimmunity. (Source, Source, Source)

What Is Autoimmunity? 

Autoimmunity is when the immune system attacks and harms its own tissues. The immune system typically works by producing antibodies against foreign invaders. These antibodies are usually able to discriminate between foreign substances and our own bodies — a mechanism known as immune tolerance. 

Even healthy people have some immune cells with autoreactivity, or the potential to attack the body’s own tissues, but these cells are normally destroyed before they can do any harm. However, if these immune cells are triggered by a genetic predisposition or environmental factors, they may lead to autoimmune disease. (Source, Source)

Autoimmune diseases affect approximately 50 million people in the United States, and include but are not limited to rheumatoid arthritis (RA), type 1 diabetes mellitus (T1DM), inflammatory bowel disease (IBD), systemic lupus erythematosus (SLE), celiac disease, and multiple sclerosis (MS). 

Many of the risk factors for developing autoimmune disorders are beyond our control, but gut health is one we can do something about. (Source

How Is Gut Health Related to the Immune System?

There is a mutually beneficial relationship between the gut and the immune system. The gut microbiota aids in the development of the immune system, while the immune system regulates interactions between the gut and the rest of the body. Alterations in  environmental factors or immune function can change the gut microbiota, which can then weaken or dysregulate the immune system. (Source)  

How Is Gut Health Related to Autoimmune Diseases?

Altered gut microbiota composition — also known as dysbiosis — can disturb the regulatory mechanisms of a healthy gut, affecting intestinal permeability, immune tolerance, and inflammatory gene production.

Dysbiosis may be associated with specific diseases, such as T1DM, MS, IBD, and obesity. However, it is not yet clear if dysbiosis causes disease, or if the diseases themselves lead to changes in gut microbiota composition and function. (Source, Source)

woman curled up holding stomach

Gut Health and Inflammatory Bowel Disease (IBD)

Inflammatory bowel disease, which includes ulcerative colitis (UC) and Crohn’s disease (CD), causes abdominal pain, diarrhea, vomiting, and bloody stool. Researchers have found IBD is associated with certain types of gut microbes as well as decreased diversity of microbes. However, it is not clear whether changes in gut microbiota cause this inflammation or vice versa. (Source, Source)

Gut Health and Rheumatoid Arthritis (RA)

Rheumatoid arthritis is an autoimmune disorder resulting in joint disability, inflammation, and deformity. There is thought to be a connection between the gut and rheumatic diseases, as arthritis is commonly found in people with IBD. Specifically, new-onset RA and psoriatic arthritis have both been associated with a specific gut microorganism, Prevotella copri, and reactive arthritis can be triggered by infections of the gut microbiota by organisms such as Salmonella. (Source)

Gut Health and Type 1 Diabetes Mellitus (T1DM)

In T1DM, immune cells attack insulin-producing cells in the pancreas, resulting in their destruction. Changes in gut microbiota are thought to be a possible predisposing factor for the onset of T1DM and were found to be involved in the progression of early incidence T1DM. In one study, children with T1DM were found to have decreased richness of one bacterial subgroup and increased richness of another, which was opposite to what was found in healthy children. (Source)

Can Digestive Issues Cause Autoimmune Diseases?

Issues within the digestive tract may be related to the onset of autoimmunity. In addition to dysbiosis, which can cause inflammation, disruption of the gut barrier can lead to increased intestinal permeability. This increased permeability, known as leaky gut, may allow toxins and pathogens to leave the gut and enter the bloodstream. It is theorized that some foreign antigens that escape the gut may trigger production of autoantibodies, contributing to the development of autoimmune disorders. (Source)

How Do I Strengthen My Gut and Immune System?

New research has shown that, for those predisposed to autoimmunity or who currently have an autoimmune disease, dietary interventions can have positive effects on the gut microbiota, intestinal permeability, inflammation, and immune response. 

Mediterranean Diet and Gut Health

The Mediterranean diet, which consists primarily of fruits and vegetables, whole grains, fish, legumes, and monounsaturated fats, has been shown to increase gut microbiota short-chain fatty acids, which help improve digestion and intestinal integrity. This diet also decreases certain risk factors of autoimmune diseases, such as gut inflammation.

Vegetarian Diet and Gut Health

Reducing consumption of animal products may also help mitigate risk factors associated with autoimmune diseases. Long-chain saturated fats found in meat may result in gut dysbiosis, increased intestinal permeability, and inflammation. Further, arachidonic acid found in animal products is pro-inflammatory. Decreasing animal product consumption can help prevent dysbiosis, maintain intestinal integrity, and has specifically been found to counteract the progression of RA joint swelling and tenderness. 

Gluten and Gut Health

Gluten is a trigger for those with celiac disease, resulting in the production of autoantibodies. For susceptible individuals, gluten is proinflammatory and contributes to dysbiosis, changes in intestinal permeability, and changes in immune regulation. A gluten free diet is an important first line of defense for those with celiac disease. (Source)

array of vegetables and starches 

Can Probiotics Help Autoimmune Diseases?

Probiotics are active bacteria that may help regulate the immune response. (Source)

The use of probiotics has not yet been approved as a treatment or prevention strategy for any health problem. A number of evidence-based reviews of the benefits of probiotic use on gut bacteria and autoimmune diseases have been done, but results have been mixed. 

For example, in some studies people with RA taking a probiotic were found to have decreased clinical symptoms and decreased inflammatory gut proteins. However, some recent studies did not report any effects of probiotics in individuals with RA. (Source)

Research continues into potential negative consequences of treatment with probiotics, as well as which probiotic strains are best for different health issues. 

Can Vitamin D Reverse Autoimmune Diseases? 

Vitamin D deficiency is associated with several autoimmune diseases including MS, T1DM, and SLE, although we don’t yet know if it is a cause or a result of these diseases. Receptors for vitamin D are found in many cells throughout the body, and it has been found to play an important role in immune function.

For this reason, vitamin D has been tested as a potential treatment for autoimmune diseases. However, larger well-controlled studies are needed to establish its clinical use and efficacy. (Source)

Vitamin D pills on yellow surface

The Bottom Line on Gut Health and Autoimmunity

The gut microbiota is inextricably linked to immune system development and regulation, as well as specific autoimmune diseases. This relationship is multifaceted, but it is possible that supporting your gut microbiota through diet could slow the development and progression of certain autoimmune diseases. 


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