“Leaky Gut” – A Key Factor in Inflammation & Autoimmune Disease


By Dr. James Yoon, ND

“Leaky Gut” – A Key Factor in Inflammation and Autoimmune Disease

Have you noticed a connection between what you eat and how you feel? We know that the foods we eat can have a profound impact on our health, but research is showing that our gut health – and its role in inflammation and autoimmune disease – is much more connected than once thought. 

The small intestine is lined with a special layer of epithelial cells that has selective permeability. It absorbs nutrients from food while preventing harmful substances (in the form of antigens) from leaving the GI tract and entering the body. When the physical barrier is disrupted – for example, from poor diet, chronic stress, alcohol consumption, recurrent antibiotic use or infections – damage can occur and lead to inflammation of the intestinal lining. If the lining becomes too damaged and inflamed, it becomes hyper-permeable. This condition is known as intestinal hyper-permeability, or leaky gut syndrome. Without an intact and properly functioning intestinal barrier, foreign antigens that are normally prevented from entering the body are able to penetrate past through the lining and get absorbed into blood and lymphatic circulation. The immune system recognizes these foreign antigens and responds by creating antibodies against them, which leads to inflammation and/or tissue damage in other organs of the body. 

When you think of leaky gut not so much as a disease, but as a mechanism of how certain conditions can develop, it starts to make sense. A leaky gut is the pathway for how toxins enter the body through the GI tract and create all kinds of mayhem once they’re in, sort of like party crashers who slip through security and proceed to make a mess of the venue. A lot of the patients I see with leaky gut have digestive issues such as chronic diarrhea, constipation, gas or bloating. However, leaky gut can be associated with a number of symptoms and health conditions, including:  

  • Nutritional deficiencies
  • Poor immune system
  • Headaches, brain fog, memory loss
  • Excessive fatigue
  • Skin rashes and problems such as acne, eczema or rosacea
  • Cravings for sugar or carbs
  • Arthritis or joint pain
  • Depression, anxiety, ADD, ADHD

The Role of Leaky Gut in Inflammation and Autoimmune Disease

Because leaky gut promotes inflammation, healthcare providers are beginning to understand how it can play a key factor in autoimmune disease. From my own clinical experience, I find that assessing for and healing a leaky gut can significantly improve autoimmune conditions where inflammation is a main factor. An autoimmune disease occurs when the  immune system makes antibodies against and attacks its own tissues. Foreign antigens (e.g. from food, bacteria, and other pathogens) can look very similar to the antigens in human tissue. In leaky gut, the immune system attacks the foreign antigens that pass into the body, but also mistakingly attacks the body’s own tissues that resemble these foreign antigens. For example, if a foreign antigen looks similar to the antigens in the joints of the hand, the immune system will create an inflammatory response and attack both of these antigens. If these food antigens continue to pass freely into the body, the immune system is constantly stimulated, leading to a condition known as auto-immune arthritis, also known as rheumatoid arthritis. Other examples of autoimmune diseases that are associated with leaky gut include celiac disease and inflammatory bowel disease, type 1 diabetes, multiple sclerosis, ankylosing spondylitis, lupus, and thyroiditis.

Lab Testing for Leaky Gut – Comprehensive Stool Analysis

A Comprehensive Stool Analysis is one of the most frequently ordered tests that I use in my clinical practice. It detects the presence of pathogenic microorganisms such as yeast, parasites, and bacteria that contribute to leaky gut. It also provides helpful information about prescription and natural products effective against specific strains detected in the sample. The test also evaluates beneficial bacteria levels, intestinal immune function, overall intestinal health, and inflammation markers.

A Comprehensive Stool Analysis is useful tool for: 

  • Gastrointestinal symptoms such as persistent diarrhea, constipation, bloating, indigestion,  and malabsorption
  • Autoimmune disease
  • Joint pain 
  • Inflammation 
  • Food sensitivities
  • Atopic dermatitis 

At Lakeside Natural Health Centre, a Comprehensive Stool Analysis kit is provided to patients so they can collect their sample in the comfort of their own home. Completed kits can be conveniently picked up by Purolator directly from home or dropped off at a Purolator location. 

The 5R Digestive Restoration Program for Leaky Gut in Autoimmune Conditions

We use a program that goes by the simple acronym of the “5Rs”: remove, replace, reinoculate, repair, and rebalance. When applied to various chronic and autoimmune conditions, the 5R program can lead to dramatic improvement in symptoms, and sometimes even complete resolution of the problem. The elements of the 5R program are described briefly below. 

1. Remove

  1. Remove things that negatively affect the environment of the GI tract including allergic foods and parasites or other bad bugs such as bacteria or yeast. This might involve using an allergy “elimination diet” or food intolerance blood test to find out what foods are causing GI symptoms, or it may involve taking drugs or herbs to eradicate a particular bug. 

2. Replace 

Replace digestive secretions like digestive enzymes, hydrochloric acid, and bile acids that are required for proper digestion and that may be compromised by diet, drugs, diseases, aging, or other factors. 


Help beneficial bacteria flourish by ingesting probiotic foods or supplements, and by consuming the high soluble fibre foods that good bugs like to eat, called “prebiotics.” Probiotics are beneficial microorganisms found in the gut that are also called “friendly bacteria.” Because antibiotics kills both good and bad bacteria, probiotics in the form of supplements and/or food are needed to help support the gut flora. Fermented foods, such as yogurt, miso, and tempeh are food sources of probiotics. Prebiotics are non-digestible food ingredients that feed probiotic bacteria to grow and thrive in the digestive tract. Food sources of prebiotics include artichokes, garlic, leeks, onion, and chicory root. Another good prebiotic source is a supplement called “fructo-oligosaccharide” or FOS. 

4. Repair 

Help the lining of the GI tract repair itself by supplying key nutrients that can often be in short supply in a disease state, such as zinc, antioxidants (e.g. vitamins A, C, and E), fish oil, and the amino acid glutamine. 

5. Rebalance 

Pay more attention to your lifestyle choices. Incorporate sleep hygiene, regular exercise, and stress management techniques into your daily routine, as these all can affect the digestive tract and immune system health. 




Fasano, A. Leaky Gut and Autoimmune Diseases. Clinic Rev Allerg Immunol (2012) 42:71–78

Mu et al. Leaky Gut as a Danger Signal for Autoimmune Diseases. Frontiers in immunology (2017 May) 8: Article 598