5 ways gut issues can lead to autoimmune disease

One of the most talked about areas regarding autoimmune diseases is the connection between the development of autoimmune conditions and gut health. Autoimmune diseases in and of themselves, such as Crohn's disease and ulcerative colitis, can affect the gut. Still, imbalances in gut health can contribute to the development of an autoimmune disease. 


The gut is a fascinating and complex ecosystem that plays a crucial role in our overall health. It's not just responsible for digesting food; it also significantly impacts our immune system, which is why it is one of the first areas I explore when working with clients with autoimmune diseases. 

Bloating, indigestion, constipation, pain, and an urgency to go to the toilet may all be signs of gut imbalances. Still, even more widespread symptoms such as skin rashes, brain fog, and fatigue may also be related to gut issues. 

In recent years, researchers have uncovered a profound link between gut issues and autoimmune diseases. This article will explore five key areas of digestive health that shed light on this intricate connection: maldigestion, dysbiosis, metabolic function, infection, and inflammation.

These five areas are all tested for in the GI Effects stool test that I offer at The Autoimmunity Nutritionist Clinic. You can find more information about The Gut Health Testing Package.

1. Maldigestion

Maldigestion is a term used to describe the improper breakdown of food in the digestive system. When food isn't digested properly, it can lead to the formation of antigens that trigger an autoimmune response. This is particularly relevant in coeliac disease, where gluten intolerance leads to an immune response against the small intestine's lining. 

Some of the critical markers for maldigestion are low pancreatic elastase and fat in the stool. 

Specific vitamins, such as vitamins A, D and E, are fat soluble, which means that without proper fat digestion, you can become deficient in these vitamins, which are essential for proper immune function and may indirectly contribute to the development of autoimmune disease.

Addressing maldigestion through dietary changes that enhance the release of stomach acid, digestive enzymes, and gastric juices is essential. Enzyme and bile supplements, which help to break down food particles, may also reduce the risk of autoimmune flares.

 2. Dysbiosis

The gut is home to trillions of microorganisms, collectively known as the gut microbiota. When the balance of these microbes is disrupted, it can lead to dysbiosis, an imbalance linked to autoimmune diseases, as it can increase intestinal permeability, leading to leaky gut syndrome. Leaky gut syndrome is considered a risk factor for autoimmune disease. 

Dysbiosis can result from various factors, including a poor diet, antibiotic use, or stress, so incorporating a nutrient-dense diet and stress management practices, such as yoga and meditation, may help to maintain a more balanced flora. 

Restoring a healthy gut microbiome through eating a diet rich in polyphenol-rich foods and prebiotics and including proteins such as glycine, which support gut barrier function, can help mitigate the risk of autoimmune disorders.

3. Metabolic function: Short-chain fatty acids

Short-chain fatty acids (SCFAs) are byproducts of bacterial fermentation in the gut. These compounds, such as butyrate, acetate, and propionate, play a crucial role in maintaining a balanced immune system. 

SCFAs help regulate inflammation, support the gut barrier, and influence immune cell behaviour. A deficiency in these metabolites has been associated with autoimmune diseases. 

Consuming fibre-rich foods and fostering a diverse gut microbiome can enhance SCFA production and support immune balance.

Stewed apples are a great source of dietary fibre that helps to increase the production of SCFAs, as when you stew apples with the skin on, it releases the fibre pectin. Pectin is an indigestible polysaccharide that human enzymes can not break down. However, they can be easily degraded by gut bacteria with the production of SCFAs, which are beneficial for gut barrier function and may help to prevent autoimmune symptoms and the development of autoimmune disease. 

4. Infection

Infections can trigger or exacerbate autoimmune diseases. Molecular mimicry is one mechanism through which infections may lead to autoimmunity. 

In this process, antigens produced by infectious agents resemble the body's own proteins, leading the immune system to attack its cells mistakenly. 

Some autoimmune conditions, such as rheumatoid arthritis, have been linked to specific infections which are found in the gut. Preventing and managing infections is crucial for those with autoimmune diseases, as they may act as triggers or worsen existing symptoms.

Autoimmune diseases are often thought of as non-infectious conditions. However, many studies support the fact that infections likely play a role in the development of autoimmune diseases both directly and indirectly. 

Supporting the immune response with omega-3 fatty acids found in oily fish and nutrient-dense foods that include vitamins A, C, D, and E are essential to maintaining a robust immune system.

5. Inflammation

Inflammation in the gut is often a precursor to autoimmune diseases. Chronic inflammation can lead to increased gut permeability, commonly called "leaky gut." 

In this state, substances that should remain in the gut, including bacteria and food particles, leak into the bloodstream, triggering an immune response. This process may lead to systemic inflammation, contributing to autoimmune diseases. 

Markers for inflammation include calprotectin, secretory IgA, and eosinophil protein X, which will provide insight into what might be driving inflammation in the gut.

Lifestyle changes, including a balanced diet, stress management, and regular exercise, can help reduce inflammation and support a healthy gut.

The connection between gut issues and autoimmune diseases is a complex and evolving field of research. Maldigestion, dysbiosis, metabolic function, infection, and inflammation all play pivotal roles in this intricate relationship. 

By gaining insights into these critical areas and their potential impact on your health, you empower yourself to adopt a personalised approach by addressing any imbalances in your gut. A harmonious gut sets the stage for a robust immune system, creating a positive domino effect for your overall well-being.

If you would like to learn more about my services and how nutritional therapy can help improve your gut health, please book a free discovery call with me

The views expressed in this article are those of the author. All articles published on Nutritionist Resource are reviewed by our editorial team.

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London W1G & Harrogate HG1
Written by V. J. Hamilton, Autoimmune Disease Expert | BSc (Immunology), DipION, mBANT
London W1G & Harrogate HG1

VJ Hamilton is a qualified Nutritional Therapist and member of BANT, focusing on autoimmunity including inflammatory skin disorders, fatigue and neurological issues as well as gut health.

VJ has a BSc in Biochemistry and Immunology which she uses in her practice, using only evidence-based nutritional therapies to support chronic conditions.

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