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Written by
Tram Pham
Medically Reviewed by
Dr. Andrea Perez

The gastrointestinal (GI) tract plays an important role in every aspect of our health, including our metabolism and immunity. Changes in environmental factors can have a negative impact on the gut microbiota, which can then weaken the immune system. Improving our gut health is often the first step toward addressing the underlying cause of our digestive issues and reducing autoimmune disease development or progression. (Source, Source

In this article, we will explore how gut health and autoimmune diseases are related, where digestive issues fit into this relationship, and how the 5R gut healing protocol can be used to help strengthen the immune system and restore gut health.

How Is Gut Health Related to Autoimmune Diseases?

The gut contains about 70%–80% of the immune cells in our body and is an essential part of the immune system. The gut microbiome helps regulate our immune system and defend against foreign substances that enter the body. Changes in the composition of the gut microbiome — also known as dysbiosis — can prevent the microbiome from functioning properly, which affects intestinal permeability, immunity, and inflammatory response. Dysbiosis may be associated with the development of autoimmunity and may be a major cause of several chronic diseases. (Source, Source)

Many of the risk factors for developing autoimmune disorders are beyond our control, but gut health is one factor we can do something about. Supporting our gut microbiome through diet and other lifestyle factors could slow the development and progression of autoimmune diseases. (Source, Source, Source)

The 5Rs of gut healing is a holistic framework developed by the Institute of Functional Medicine to address a variety of GI issues, including irritable bowel syndrome, small intestinal bacterial overgrowth (SIBO), gastroesophageal reflux disease, celiac disease, and inflammatory bowel disease (ulcerative colitis and Crohn’s disease).

If you are struggling with gut health issues and don’t know where or how to start healing them, the 5R gut healing protocol can provide you with actionable steps to help kickstart your gut health journey. (Source) Here’s how to begin.

1. Remove

The first step is to remove anything that could be irritating your gut. Adopting an elimination diet, such as the autoimmune protocol (AIP) diet, or using a food sensitivity test may be helpful in identifying foods that are causing you problems. Navigating trigger foods can be overwhelming. Our Care Team at WellTheory can help guide and support you through the process of removing trigger foods sustainably. (Source)

Some common gut irritants include: 


  • Alcohol, coffee, processed food, and food additives are known to irritate the gut lining and cause digestive issues. (Source, Source)
  • Food sensitivities or intolerances (the most common culprits are gluten, dairy, soy, and sugar) make it hard for your body to digest certain foods.  (Source, Source)


  • Nonsteroidal anti-inflammatory drugs (NSAIDs), such as aspirin and ibuprofen, can disrupt the intestinal barrier. (Source)
  • Antibiotics can change the composition of the gut microbiome and stimulate an inflammatory response. (Source)


  • Stress has a direct impact on gut permeability. Stress causes the release of cortisol, our body’s stress hormone, which can damage the gut lining and lead to systemic inflammation. (Source, Source)


  • Infections such as SIBO, yeast overgrowth, and parasites can lead to poor absorption of nutrients. (Source)

Elimination diets require removing a number of nutritious foods from your diet for several weeks or months, so it’s best to consult with a nutritional therapy practitioner, dietician, or other health care practitioner before starting one. They will help ensure proper nutrient density and monitor your diet and its effects on your health. 

2. Replace

Next, replace missing elements that are critical for proper digestive function. (Source)

Elements to kickstart your digestive system include: 

  • supplements that help the body digest (break down) food more easily, such as hydrochloric acid (HCl), bile salts, and digestive enzymes 
  • foods that help your body produce these missing elements. For example, bitter foods such as dandelion greens help stimulate stomach acid and digestive enzymes. (Source)
  • foods and/or supplements that address nutrient deficiencies in your body. For example, bone broth contains amino acids that help heal the gut lining, and cold water fish contain omega-3 fatty acids that help reduce inflammation. (Source)

3. Reinoculate

The third step is to reinoculate your gut with beneficial bacteria via fermented foods, probiotics, and prebiotics to restore a healthy, balanced microbiome. (Source)

Remember, elimination diets are temporary! Once your symptoms have improved, it’s important to add nutrient-dense, inflammation-reducing foods back into your diet.

The following types of foods can help rebalance good bacteria:

  • Prebiotic foods are those that gut bacteria love to eat. They can be found in dietary fiber, which is the indigestible part of many plants. For example, fruits, vegetables, and legumes are all excellent sources of prebiotic fiber. (Source)
  • Probiotic foods are those rich in bacteria that keep the gut microbiome healthy and may help regulate the immune response. They can be found in fermented foods and beverages such as yogurt, sauerkraut, kimchi, and kombucha. (Source)

4. Repair

The fourth step focuses on repairing the gut lining. Digestive conditions can affect the absorption of nutrients, so flooding the body with key nutrients can help reduce inflammation and address nutrient deficiencies. (Source)

Key nutrients to incorporate include:

  • foods high in calcium, magnesium, zinc, iron, omega-3s, and vitamins A, C, D, and B12, which are beneficial to digestive function (Source)
  • foods rich in collagen, such as bone broth, eggs, and chicken, which are good sources of amino acids (e.g., glycine, hydroxyproline, proline, and alanine) and protect and maintain the intestinal barrier (Source) 
  • herbs and supplements such as L-glutamine, aloe vera, and turmeric, which are anti-inflammatory and boost gut health (Source, Source, Source)

5. Rebalance

The final step is to rebalance, which is all about lifestyle. Your lifestyle habits — sleep, diet, emotions, physical activity, and stress levels — all have an enormous influence on your digestive function and health. 

During this stage, you’ll want to focus on stress management. Stress can be caused by many things, such as relationships, work, lack of sleep, and overexertion (from exercise or other aspects of life). Increased stress can increase cortisol levels, which affects your metabolism, and in turn, your digestive function. While you can’t always remove stressors, you can support your body to better manage stressful events when they arise. 

There are a number of steps you can take to lower cortisol, including:

  • making changes to your diet, adding dietary supplements (e.g., ashwagandha, magnesium glycinate), and adopting healthy lifestyle changes (Source, Source)
  • incorporating stress-reducing practices, such as meditation, mindfulness, deep breathing, and restorative yoga into your routine (Source, Source)

The Bottom Line on the 5R Gut Healing Protocol

Healing the gut often requires eliminating the root causes that trigger your symptoms and managing those triggers through dietary and lifestyle interventions.

The 5R protocol is a holistic framework used to address digestive issues and restore gut health. The first step is to remove anything that could be irritating to the gut. The second step is to replace missing elements or nutrients that are key to proper digestion and absorption. Once your symptoms have improved, the third step is to reinoculate your intestinal tract with beneficial bacteria that make up the microbiome. The fourth step is to repair your gut lining with key nutrients that reduce inflammation and promote digestion and absorption. Finally, the last step is to rebalance your lifestyle to maintain the improvements to your symptoms and support a healthy mind and body.

Remember, the main goal of a gut healing protocol is to nourish the body and improve its ability to heal itself through a holistic, well-balanced, and personalized approach. If you have already made all of these changes and don’t see any improvements to your digestive issues, it’s best to consult with a health care practitioner to help you manage your symptoms. At WellTheory, our Nutritional Therapy Practitioners are experienced with supporting those with gut imbalances and helping you navigate your health journey with confidence. Learn more about how we can support you here.

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