Top 6 Autoimmune Triggers You Can Control: Leaky Gut

“A well functioning gut with healthy gut flora holds the roots of our health. And, just as a tree with sick roots is not going to thrive, the rest of the body cannot thrive without a well-functioning digestive system.”

– Dr. Natasha Campbell-McBride, Neurologist, Neurosurgeon, Nutritionist & Author of Gut and Psychology Syndrome

Accumulating research shows that there are many environmental factors that contribute to autoimmune conditions. The Top 6 Autoimmune Triggers You Can Control series helps simplify the seemingly endless potential triggers into 6 major autoimmune trigger categories I call F.I.G.H.T.S.™:

Top Autoimmune Trigger: Leaky Gut

In this second post in the Top 6 Triggers series, I highlight leaky gut and imbalanced gut bacteria (dysbiosis) and the science that confirms their involvement in the development of autoimmune and other chronic disorders. Then I share steps to help you address gut health naturally and effectively so you can get on the path back to health.

Let’s start with the great news:

Groundbreaking Research Shows Leaky Gut Is Key to Autoimmunity

In 2012 Alessio Fasano, MD, Chief, Division of Pediatric Gastroenterology and Nutrition at Massachusetts General Hospital (Mass Gen) & Director, Center for Celiac Research, and his team published their breakthrough research findings1, revealing the third element in the equation necessary for the development and perpetuation of most autoimmune disease: the loss of intestinal barrier function, a.k.a., “leaky gut syndrome,” or just “leaky gut” for short.

We now know that three conditions must be in place to cause and perpetuate virtually all autoimmune disorders:

  1. A genetic predisposition to autoimmunity
  2. Exposure to one or more environmental trigger (think F.I.G.H.T.S.™)
  3. Increased intestinal permeability (aka a “leaky gut”)

This is fantastic news for anyone dealing with an autoimmune condition. Dr. Fasano sums up why:

“Once the autoimmune process is activated, it is not auto-perpetuating, rather [it] can be modulated or even reversed by preventing the continuous interplay between genes and environment.”2 

— Alessio Fasano, MD

Thanks to Dr. Fasano’s findings we now have equations for both developing and reversing autoimmune conditions.

The path to autoimmunity:


The path to health:

Leaky Gut Leads to Illness: 3 Stories

Multiple Sclerosis (MS): My Story

I suffered symptoms of numbness, tingling, pain, tightness, heaviness, blurred vision and fatigue due to flare-ups of Multiple Sclerosis (MS) for 26 years before identifying my lynchpin triggers. I had no idea that my chronic mild digestive discomfort had anything to do with the MS. I just thought that it was normal to feel some tummy rumbling after meals.

In 2010 I saw a Functional Medicine nutritionist who ran some tests.  Functional Medicine is root cause medicine and it’s all about detecting imbalances as early as possible. In contrast to standard lab tests which help doctors decide which drugs to prescribe for symptoms of disease, Functional Medicine tests detect early disease markers, allowing for correcting and optimizing function at the root cause level as soon as possible.

My test results revealed that I had both non-celiac gluten sensitivity (NCGS) and sensitivity to casein, an inflammatory protein found in animal dairy, especially A1 Holstein cows. A stool test revealed I had both dysbiosis (gut flora imbalance) and significantly low levels of immune-protective, secretory IgA (sIgA), which indicated lack of integrity of my intestinal mucosal lining. In other words, I had an imbalanced and leaky gut.

The nutritionist advised me to eliminate gluten and cow dairy from my diet and led me through a 30-day gut-healing protocol, including a comprehensive elimination diet and a leaky gut repair supplements. Within a week I stopped experiencing digestive distress following meals, and within a month I stopped having MS symptoms completely. To this day, twelve years later, I have never again experienced a single MS symptom. A blood test later confirmed that my antibody levels against myelin sheath (Cyrex Labs 7x) were completely in the normal range, which meant my immune system was no longer attacking my myelin sheath. I no longer had MS. To be clear, I will always have the genes for MS, but those genes don’t need to be EXPRESSED.

Autism: Sam’s Story

Sam, a 2½-year-old diagnosed with autism, was brought in to see functional medicine pioneer, Mark Hyman, MD. Sam had been happy and healthy until he had his measles, mumps, and rubella (MMR) vaccination at 22 months. Dr. Hyman explains that some people are especially sensitive to the vaccine preservative, thimerosal (ethylmercury). Sam lost his language function, became detached and unable to relate to his parents and friends.

Dr. Hyman ordered functional tests and found that Sam had high levels of antibodies to gluten, dairy, eggs and soy — common autoimmune food triggers. Sam also had a leaky and inflamed gut. Dr. Hyman had Sam’s parents remove the triggering foods and add in gut healing supplements: digestive enzymes, probiotics, zinc, magnesium, folate, vitamins A, B6, B12, D3, and fish oil. According to Dr. Hyman, “After 10 months, Sam’s bowels were back to normal, he was verbally fluent, mainstreamed in school and he ‘lost’ his diagnosis of autism.”

Persistent Brain Fog, Headaches, Insomnia & Obesity: Shoshana’s Story

Shoshana, a 40-year old patient of Raphael Kellman, MD, author of The Microbiome Diet, was afflicted with frequent insomnia, headaches, near-constant brain fog and a persistent extra 20 pounds. Dr. Kellman knew that Shoshana was almost certainly facing two problems: an imbalanced gut microbiome and a leaky gut. Both conditions set Shoshana up for chronic inflammation, an overactive immune system and a fat-storing metabolism. On the autoimmune spectrum, these symptoms are common with the autoimmune expression phase which precedes full-blown autoimmune disease.

Dr. Kellman had Shoshana follow a “4R Protocol” to 1. Remove the top triggering foods: eggs, dairy, soy, gluten, and grains; 2. Replace missing stomach acid and enzymes; 3. Reinoculate her microbiome with needed pre- and probiotics, and 4. Repair the leaky gut barrier with healing minerals, foods and anti-inflammatory supplements. By the time Shoshana completed the 4R gut-healing program, her symptoms disappeared along with her unwanted weight.

How a Leaky Gut Leads to Poor Health

More than 2,500 years ago, Hippocrates observed that “all disease begins in the gut,” and science now confirms that there is a critical and delicate interplay between our intestinal integrity, our environment, and our health and wellbeing. When gut balance is disrupted and/or the intestinal barrier is compromised, health and wellbeing suffer.3

Leaky gut refers to a damaged or compromised intestinal lining (epithelium) and atrophied “microvilli.” When the intestinal lining is damaged due to any number of inflammatory substances — SAD or processed foods, toxins, stress, infections — the “shag carpeting” (microvilli) becomes worn down, resembling “Berber” carpeting, and the intestinal “tight junctions” loosen. The lining that normally functions like a fine sieve becomes more like a torn fishing net – allowing large, undigested particles — including bacteria, incompletely digested proteins and toxins — to pass through the gut lining and into the bloodstream, where they don’t belong.

When pathogenic (“bad”) bacteria outnumber the good, the gut lining can become inflamed and leaky. Nutrients are not properly absorbed, the creation of the feel-good neurotransmitter, serotonin, is disrupted, and a vicious cycle persists until the health of the gut lining and bacterial balance are restored.

Leaky Gut and Immune System Activation

Once the undigested foods and toxins enter the bloodstream, the immune system – just doing its job — tags those particles as “dangerous invaders” and creates antibodies (soldiers) to attack them.  A cascade of immune reactions follows. Food sensitivities, malabsorption, nutrient deficiencies, systemic inflammation and even breaching of the blood-brain barrier become common. The immune system can become confused and attack the body’s own tissue — which is the initiation of autoimmune processes.4

Signs that You Have a Leaky Gut

If you have autoimmune issues or any of the symptoms below, chances are that you have gut issues too — and here’s the clincher: whether or not you feel gut symptoms:

  • Abdominal discomfort
  • Anemia
  • Anxiety
  • Arthritis
  • Asthma
  • Autism
  • Bloating after meals
  • Brain fog
  • Celiac disease
  • Chronic inflammation
  • Chronic pain
  • Colitis
  • Constipation
  • Dementia
  • Depression
  • Diarrhea
  • Eczema
  • Fatigue
  • Food cravings (especially sugar and carbs)
  • Food sensitivities
  • Gastrointestinal (GI) issues
  • Headaches
  • Hypersensitivity
  • Insomnia
  • Inflammatory Bowel Disease (IBD)
  • Irritable Bowel Syndrome (IBS)
  • Learning challenges
  • Lethargy
  • Migraines
  • Mouth sores
  • Psoriasis
  • Sinus conditions
  • Skin conditions (acne, eczema, hives, psoriasis, rosacea)
  • Undigested food in stool
  • Weight loss resistance

The Many Causes of Leaky Gut

The inflammation that leads to leaky gut can be caused by many factors, sometimes in isolation but often in combination. For me the inflammatory combo was sugar, gluten, dairy, Candida overgrowth, mercury toxicity from multiple fillings, and chronic stress. For other people it could be nuts and nightshade vegetables (tomatoes, white potatoes, eggplant, and peppers); or perhaps overuse of antibiotics and other prescriptions meds.

  • Standard American Diet (SAD): processed oils, flours, sugar
  • Biggest food triggers: gluten, dairy, grains
  • GMO (genetically modified organisms) foods
  • Foods sprayed with or engineered with glyphosate (RoundUp)
  • Soda (regular and diet)
  • Excessive alcohol or caffeine consumption
  • Pain relievers (steroids, ibuprofen, acetaminophen, aspirin)
  • Antibiotics, antacids & prescription medications
  • Stress & unresolved emotional trauma
  • Birth control pills
  • Smoking
  • Chemotherapy & radiation
  • Oxidative stress (intracellular damage)
  • Heavy metals: mercury
  • Infections: bacterial, viral, fungal, parasites
  • Toxins: chemicals, pesticides, bacterial waste

Studies Link Leaky Gut with Autoimmune Issues

  • Gut Dysbiosis

    Disruption of the intestinal ecosystem balance, known as gut dysbiosis, is associated with many chronic conditions, including autoimmune disorders and allergic diseases.5

  • Stress

    Chronic or acute stress adversely affects the balance of bacteria in the gut, and this has profound implications on our immunity. Stress can lead to changes in composition, diversity and number of gut microorganisms. 6

  • Type 1 Diabetes

    Increased intestinal permeability has been observed in animal models of Type 1 diabetes (T1D) as well as in humans with, or at increased-risk for, the disease. 7

  • Crohn’s Disease

    Researchers found that microbial balance was disrupted in patients with Crohn’s disease, with beneficial microbes missing and pathogenic microbes flourishing.8

  • Rheumatoid Arthritis (RA)

    New evidence shows a correlation between the onset of rheumatoid arthritis (RA) and the prevalence of a certain microbe—Prevotella copri9

5 Strategies to Heal Your Gut

Get the Data

If you are dealing with any of the symptoms above, and/or an autoimmune condition, chances are very good that you would benefit from a gut-repair “5R protocol” (see below). If you’d like more data consider getting a Leaky Gut blood test to confirm your suspicions. Vibrant Wellness’ Wheat Zoomer panel offers a comprehensive test that bundles in leaky gut markers, celiac risk and wheat and gluten antibodies.

Follow a “5R” Gut Repair Program
The 5R program adds another “R” to the standard 4R protocol, addressing the importance of a balanced life.  
  • Remove harmful substances. This is a BIG category and includes yeast, parasites and harmful bacteria, and immune-reactive SAD and suspect foods like gluten, dairy, processed food, sugar, white table salt, grains (e.g., wheat, rye, barley, oats, corn, quinoa, etc.), legumes (e.g., lentils, peanuts, soy), tree nuts, eggs, coffee and alcohol.
  • Replace immune-reactive foods with nourishing foods like above-ground vegetables, healthy fats like avocados, olive and coconut oils, ghee (clarified butter without the allergens), organic, pastured meats, wild fish, and berries. Replace missing digestive enzymes & stomach acid.
  • Reinoculate the gut with missing beneficial bacteria by using probiotics and prebiotics — fiber that those probiotics eat.
  • Repair the gut lining with targeted nutrients: L-glutamine powder, zinc, pantothenic acid (vitamin B5), vitamin A, licorice root (DGL), aloe vera juice (inner aloe plant filets only), and essential fatty acids.
  • Rebalance your life with more movement, better sleep & less stress.
Keep A Food Symptom Journal

Record what you eat at each meal (don’t forget snacks and beverages!) and keep a log of physical symptoms. Note that symptoms may be immediate or delayed and may include gut distress, brain fog, headaches, acid reflux, sleeping issues, joint pain, etc. Keep track for several weeks, then review your journal to see if you can identify patterns that might point to food sensitivities.

Eat Fermented Foods

Regular consumption of cultured superfoods introduces beneficial microbes into the digestive tract to aid digestion and detoxification, provide enzymes, vitamins and minerals, and boost immunity. Fermented foods include sauerkraut, coconut kefir, and kimchi (Korean fermented vegetables).10

Eat Gut-Nourishing Foods

Remove gut-harming foods for good. Add the following gut-nourishing foods: Bone broth contains collagen and the amino acids proline and glycine; Grass fed ghee — clarified butter without the allergens casein, lactose and whey; Coconut products are made up of easy to digest medium-chain fatty acids (MCFAs), which efficiently convert into energy and stimulate the body’s metabolism — think fat loss, not fat storage; Sprouted raw seeds like chia, flax and hemp are great sources of fiber that can help support the growth of beneficial bacteria.

Let’s recap how we develop an autoimmune condition:

How do we heal?

Simple steps, but the devil’s in the details. What can you do to address your gut health? Consider one inflammatory thing to remove and one nourishing thing to add in today.

Take good care!

P.S: Want my help reversing an autoimmune condition?

If you live in the continental U.S. and are ready, willing, and able to invest in your best health, I offer Functional Medicine Total Health Transformation Programs over Zoom in collaboration with a skilled naturopathic doctor (ND). Get on my calendar for a free 30-minute discovery call.
Image Credit: Ohmega1982/Shutterstock
1 Zonulin, regulation of tight junctions, and autoimmune diseases, A. Fasano, Zonulin, regulation of tight junctions, and autoimmune diseases, Reference
2 Leaky Gut & Autoimmune Diseases, A. Fasano, Clinical Reviews in Allergy & Immunology, DOI 10.1007/s12016-011-8291-x, Reference
3 Think Twice: How the Gut’s “Second Brain” Influences Mood and Well-Being, Adam Hadhazy, Scientific American, Reference
4 Mechanisms of disease: the role of intestinal barrier function in the pathogenesis of gastrointestinal autoimmune diseases; A. Fasano, et al., Nat Clin Pract Gastroenterol Hepatol.; 2005 Sep;2(9):416-22; Reference 
5 Gut microbiota: next frontier in understanding human health and development of biotherapeutics; Prakash, S., et al.; Reference
6 Exposure to a social stressor alters the structure of the intestinal microbiota: Implications for stressor-induced immunomodulation; Bailey, M.T., et al., Brain, Behavior, and Immunity, 2011; 25 (3): 397 DOI: Reference 1 Reference 2
7 The “Perfect Storm” for Type 1 Diabetes, The Complex Interplay Between Intestinal Microbiota, Gut Permeability, and Mucosal Immunity; Vaarala, O., et al.; Reference
8 The treatment-naive microbiome in new onset Crohn’s Disease; Gevers, D., et. al.; Cell Host & Microbe, March 2014 DOI: 10.1016/j.chom.2014.02.005 Reference
9 Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis, Scher, J., et. al, Reference
10 Caroline Barringer, NTP, CHFS, FES Reference




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Palmer is a certified Functional Medicine Health Coach who has helped thousands of people reverse autoimmune conditions based on her own two-decade battle to successfully beat multiple sclerosis (MS). She’s the author of the Amazon #1 bestselling book, Beat Autoimmune, which has a powerful foreword by Functional Medicine pioneer, Mark Hyman, MD.

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