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The Connection Between Gut Health and Autoimmune Disease

July 20, 2023

Dr Auto Immune

The intricate relationship between gut health and autoimmune diseases has garnered significant attention in recent years. Scientific studies have unveiled the impact of a healthy gut on the immune system, revealing how imbalances in the gut microbiome can contribute to the development and progression of autoimmune disorders. In this blog post, we will delve into the connection between gut health and autoimmune disease, explore the symptoms, discuss the role of probiotics and supplements, and shed light on the autoimmune diet for gut repair. Furthermore, we will highlight how functional medicine practitioners like Dr. Autoimmune can play a crucial role in treating gut problems associated with autoimmune diseases.

Autoimmune Digestive Symptoms:

Autoimmune digestive symptoms can manifest in various ways, depending on the specific autoimmune disorder. However, some common symptoms include abdominal pain, bloating, diarrhea, constipation, nausea, and changes in appetite. These symptoms are often associated with conditions such as celiac disease, Crohn’s disease, ulcerative colitis, and irritable bowel syndrome (IBS).

The digestive tract is particularly susceptible to autoimmune attacks due to its dense concentration of immune cells (70% of the immune system is found here).

How Supplements & Probiotics Can Help With Gut health And Autoimmune Disease

Supplements and probiotics can play a role in supporting gut health and potentially improving symptoms of autoimmune diseases. Here’s how they can be beneficial:


Probiotics are live microorganisms that can provide health benefits when consumed in adequate amounts. They help maintain a healthy balance of gut bacteria and promote digestive health. Some ways probiotics can help with gut health and autoimmune diseases include:

  1. Restoring Gut Microbiota: Imbalances in gut bacteria (dysbiosis) have been associated with autoimmune diseases. Probiotics can help restore a healthy gut microbiota by increasing the abundance of beneficial bacteria, reducing harmful bacteria, and improving the gut barrier function (remember that most probiotics only last up to 7 days in the gut so regular use is critical).

  2. Modulating the Immune System: Probiotics can influence the immune system, helping to regulate immune responses and reduce inflammation. This modulation of the immune system may be beneficial in managing autoimmune diseases where the immune system mistakenly attacks healthy tissues. This is achieved through stimulation of specific cell groups called “T regulatory cells” ‘, which act as the symphony conductors – specific strains can increase the expression and production of these critical regulators.

  3. Improving Digestive Function: Probiotics can enhance digestion and nutrient absorption, leading to better overall gut health. Improved digestion can alleviate symptoms such as bloating, gas, and constipation, which are common in autoimmune diseases.

  4. Competing with the bad guys: Specific strains can actually kick the bad guys out, or a simple analogy I like is “occupy the parking spots”, which means the bad guys dont get access and have to move on down the line. This can be achieved through specific strains found in our GIT Power supplement.


While a balanced diet should be the primary source of nutrients, certain supplements can support gut health and alleviate symptoms associated with autoimmune diseases. Here are a few examples:

  1. Omega-3 Fatty Acids: Omega-3 fatty acids have anti-inflammatory properties and can help reduce inflammation in autoimmune diseases. They are found in fatty fish, flaxseeds, and chia seeds. Omega-3 supplements can provide additional support in managing inflammation.

  2. Vitamin D: Low levels of vitamin D have been associated with autoimmune diseases. Adequate vitamin D levels are important for immune function and can help regulate the immune system. Supplementing with vitamin D may be beneficial, especially in individuals with deficiencies.

  3. Glutamine: Glutamine is an amino acid that plays a crucial role in maintaining the integrity of the intestinal lining. It can help repair and strengthen the gut barrier, which can be compromised in autoimmune diseases. Glutamine supplements may aid in gut healing.

  4. Digestive Enzymes: Some autoimmune diseases can affect the production of digestive enzymes, leading to poor digestion. Digestive enzyme supplements can assist in breaking down food and improving nutrient absorption.

It’s important to note that the effectiveness of supplements and probiotics can vary from person to person.

The Autoimmune Diet for Gut Repair:

Diet plays a pivotal role in maintaining gut health and managing autoimmune diseases. An autoimmune diet, also known as an elimination or anti-inflammatory diet, focuses on removing potential triggers that can exacerbate symptoms. This diet typically involves a paleo diet with an emphasis on nutrient density and avoidance of processed foods to support overall health and well-being.

The fundamental principle of the paleo diet is to consume foods which include lean meats, fish, fruits, vegetables, nuts, and seeds and is often recommended to address underlying imbalances or dysfunctions in the body.

Nutrient density is a key concept in the paleo diet. It refers to the concentration of essential nutrients, such as vitamins, minerals, antioxidants, and phytochemicals, in a given food.

Whole, unprocessed foods such as organic meats, wild-caught fish, vegetables, fruits, nuts, and seeds are typically encouraged in the functional medicine paleo diet. These foods are rich in essential nutrients and generally do not contain added sugars, artificial additives, or unhealthy fats.

Processed foods, on the other hand, are generally avoided in the paleo diet. These include foods that undergo significant processing, such as refined grains, packaged snacks, sugary beverages, and artificial sweeteners.

Processed foods often lack essential nutrients and may contain additives, preservatives, and unhealthy fats, which can contribute to inflammation and various health issues.

By avoiding processed foods and focusing on nutrient-dense whole foods, the functional medicine paleo diet aims to support a healthy immune system, improve gut health, regulate blood sugar levels, reduce inflammation, and provide the necessary nutrients for optimal bodily functions.

It’s important to note that individual dietary needs may vary, and consulting with a functional medicine practitioner like Dr. Autoimmune can provide personalized guidance for adopting the paleo diet.

Can Probiotics Help Autoimmune Disease?

Probiotics have shown promise in managing autoimmune diseases by modulating the immune response and reducing inflammation. Studies have suggested that probiotic supplementation may alleviate symptoms in conditions such as rheumatoid arthritis, multiple sclerosis, and inflammatory bowel disease. However, the effectiveness of probiotics can vary depending on the individual and the specific autoimmune disorder.

The Impact of Gut Health on Autoimmune Disease:

Emerging research has highlighted the profound impact of gut health on autoimmune diseases. The gut microbiome, a complex ecosystem of microorganisms residing in the digestive tract, plays a crucial role in immune system regulation. When the balance of gut bacteria is disrupted, it can lead to a condition known as dysbiosis, triggering an inflammatory response and potentially contributing to autoimmune disorders. Improving gut health through lifestyle modifications, diet changes, and targeted interventions can positively influence the course of autoimmune diseases.

Autoimmune Disease Related to Gut Health:

Several autoimmune diseases have been associated with gut health disturbances. Celiac disease, for example, is triggered by the ingestion of gluten, a protein found in wheat, barley, and rye, which can cause intestinal damage and impair nutrient absorption.

Other conditions, such as Crohn’s disease and ulcerative colitis, collectively known as inflammatory bowel diseases (IBD), involve chronic inflammation in the gastrointestinal tract.

Additionally, some studies have indicated a connection between gut health and autoimmune conditions like rheumatoid arthritis and systemic lupus erythematosus.

Functional Medicine Approach:

Functional medicine practitioners like Dr. Ian Hollaman, also known as Dr. Autoimmune, take a comprehensive approach to diagnose and treat autoimmune diseases associated with gut health. They aim to address the root causes of symptoms by considering factors such as diet, lifestyle, stress, and gut dysbiosis.

Through thorough evaluations, personalized treatment plans, and an emphasis on patient education, functional medicine practitioners like Dr. Autoimmune can help individuals optimize an individual’s gut health and manage autoimmune diseases more effectively.

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