Leaky Gut Syndrome and Its Intersection with Dysbiosis and Autoimmunity

Autoimmune disease occurs when the immune system attacks the body itself.  Multiple Sclerosis and Hashimoto’s Thyroiditis are two examples. In MS, the immune system attacks the myelin sheath that surrounds the nerves of the body.  In Hashimoto’s Thyroiditis, the immune system attacks and destroys the thyroid gland.   For a long time, the assumption was that these diseases were fated by genetics and we had little control over their contraction or treatment.  It is interesting to note, that the huge surge in autoimmune diseases happening now is occurring almost exclusively in developed countries. (Hyman, 2010) Why are we getting so much sicker when it comes to autoimmunity?  Diet and lifestyle are the keys to that puzzle.

Epigenetics is the study of how environmental and lifestyle factors can literally switch on the genetic susceptibilities for disease.  We may be genetically predisposed to something, but without the environmental and lifestyle triggers, that gene may or may not be turned on.  Many experts believe that the root of all autoimmune disease is Leaky Gut Syndrome (LGS.)  In LGS, the intestines are compromised and literally become the entry point for toxins because they become permeable.  LGS is also known as intestinal permeability. Toxins and other antigens leak into the bloodstream via this compromised intestinal barrier and trigger autoimmunity with its hallmark rampant inflammation and oxidative damage.  If LGS is the root cause of autoimmune disease, healing the intestinal permeability can stop and even reverse (some, if not all) of the autoimmune damage.  (Ballantyne, 2014)

This a huge topic, but in this post, I set out to show how Leaky Gut Syndrome (LGS) and the closely related state of gut dysbiosis, set the stage for autoimmunity to be triggered.  I also outline ways to use nutrition to heal LGS and dysbiosis and thereby improve autoimmune symptoms. I am certified as a Paleo Autoimmune Health Coach® and as a  Wahls Protocol® Health Professionals.  Both of these protocols are focused on healing the gut and improving autoimmune symptoms.

Let’s look more closely at what LGS is and how it forms. Our largest interface with the world is our digestive system. It is one long continuous tube that starts with the mouth and ends with the anus. This tube is known as the digestive tract. The surface area of our small intestine alone covers a tennis court.  The small and large intestines are where the majority of digestion and all of the absorption happen.  One function they serve that we don’t think about often is the extremely important job of keeping the “outside” out and bringing into the body the good nutrients we need.  Just as necessary nutrients (hopefully) pass through the intestines, so do all manner of undesirable substances like processed “foods” full of chemicals, toxins from agriculture, chlorinated and fluoridated drinking water, pharmaceuticals, “bad” bacteria, waste products, and more.

Leaky Gut Syndrome is a major gastrointestinal disorder that means chronic inflammation of the intestinal lining has caused microscopic openings in the lining of the gut.  This permeability allows particles to pass through that normally would not. Amazingly, a single layer of specialized cells called enterocytes, separate our intestines and the blood, lymph, and specialized immune cells that lay just beyond.  Enterocytes have 2 functions—keeping unwanted molecules inside the intestines and transporting the needed nutrients across for our body to use.  When they are damaged or the proteins that form the tight bond between enterocytes is broken, LGS ensues. (Ballantyne, 2014) Imagine enterocytes as neatly aligned soldiers standing guard. When LGS occurs, some of those guards cannot function and there are gaps between them.

Knowing that the digestive tract is our body’s gatekeeper between “us” and the outside world, it makes sense that 80% of our immune system is in our digestive tract. (Mercola, 2008) A large part of this immune force is housed within the small and large intestines themselves.  Our gut microbes, of which an individual may have 500-1,000 different species, outnumber our cells 10 to 1. They are collectively called gut microbiota or the gut microbiome. (Ballantyne, 2014) All of the microbes living in our digestive tract, on our skin, and on our mucous membranes are referred to as our microbiome. Instead of thinking about ourselves as humans apart from other life forms, we should more accurately consider ourselves a living system, much like a garden.

A large part of our immune system is the gut microbiome. The importance of it cannot be understated. Our gut microbiota help us digest food, fight off pathogens, and even produce Short Chain Fatty Acids that provide fuel and rejuvenation for cells in the large intestine—among other functions.  The “good guys” in the gut microbiome are also called probiotics because they are so beneficial. Our microbiome is as unique to us as a fingerprint and is greatly and quickly altered by environment and lifestyle.  It dictates much of our health and the onset of many diseases. (Mercola, 2015) When the gut microbiome is unbalanced and not functioning properly, we refer to that state as dysbiosis.  Dysbiosis and LGS go hand in hand.  Many of the causes overlap.  Many consider dysbiosis to precede and be a defining factor in creating LGS.

The other major part of the immune system centered in the gut is referred to as GALT (gut-associated lymphoid tissue.)  Remember that just beyond the intestinal layer of enterocytes lie specialized gut immune cells and lymph vessels as well.  As antigens slip through the leaky gut (or even sometimes through a healthy one,) these immune cells mount an immune response.  As more and more antigens leak through, the immune system ramps up and up to rise to the growing challenge.  Inflammation occurs as the body responds to the threat.  (Ballantyne, 2014)

For some pathogenic substances, this triggers the innate immune system and causes generalized inflammation throughout the body. Other leaked antigens (like incompletely digested proteins) cause a response of the adaptive immune system. Here is an example:  Immune cells encounter an undigested soy protein and activate the adaptive immune system.  An antibody to that specific protein is secreted and a classic allergy (IgE antibody) or intolerance (IgA, IgD, IgM, or IgC antibody) to soy occurs. (Ballantyne, 2014)

Due to dysbiosis and then LGS, the stage is now set for autoimmune disease.  Antigens are now present due to the permeable gut. The immune system is trying to keep all these invaders under control, but it is more and more taxed.  With a genetic predisposition present, the immune system chemically “misreads” an antigen as our own tissue.  An antibody to that tissue is formed.  The immune system, in its heightened and confused state, then attacks those tissue it believes are invaders.

Much of our health truly does begin and end in our gut.  Here are the causal factors for Leaky Gut Syndrome and gut dysbiosis: (Bauman 2015, except where noted)

  • Poor diet (refined carbohydrates, processed foods, sugar, food additives and preservatives, low vegetable and fruit intake, gluten, and other inflammatory foods)
  • Parasitic infections
  • Chronic stress
  • Poor sleep
  • Low Vitamin D level (Assa, 2014)
  • Toxins (farming chemicals, parasites, alcohol, pharmaceuticals particularly NSAIDS, steroids, and birth control pills, chemo, radiation, heavy metals, etc.)
  • Gut dysbiosis—brought on by all of the above, plus reasons of non-exposure to beneficial bacteria:
    • not being breastfed and/or born vaginally
    • overly sterile environments (Mercola, 2014)
    • not eating fresh foods (from the garden) (Miller, 2015)
    • not spending time in nature (interacting with soil and animal microbiomes) (Miller, 2015)


The symptoms of Leaky Gut Syndrome: by no means a definitive list, but some of the more common symptoms (Bauman, 2015)

  • Chronic abdominal pain
  • Bloating, gas, constipation, diarrhea
  • Bowel diseases
  • Thyroid Problems
  • Fatigue
  • Chronic joint and muscle pain
  • Headaches, poor concentration “brain fog,” mood problems
  • Autoimmune conditions
  • Food allergies and sensitivities
  • Eczema and/or hives
  • Asthma


The “4R” approach is used to heal LGS.  The R’s stand for: (Liska, 2004)

  • REMOVE: toxins and allergens are removed. There are different elimination diet approaches to healing Leaky Gut Syndrome Like SCD (Specific Carbohydrate Diet,) GAPS (Gut and Psychology Syndrome,) Wahls Paleo Protocol, and Paleo AIP (Autoimmune Protocol.)  The Paleo Autoimmune Protocol may be the most comprehensive. After healing occurs, foods can be slowly reintroduced to check for reactivity.
  • REPLACE: replenish enzymes and other digestive factors inhibiting good digestion. This will require testing and doctor supervision.
  • REINOCULATE: introduce healthy gut microbiota through food and supplementation. Probiotic-rich foods are essential here as well as targeted supplementation.  Consuming prebiotics foods (which are food sources for beneficial gut bacteria) is important as well.
  • REPAIR: nutritional support of the gut lining. While some supplementation is warranted, nutrition plays a key role here.  Here is a list of the nutrients of major importance in intestinal wall structure and function.
    1. Vitamins—C, E, A/beta-carotene
    2. Minerals—Zinc and manganese
    3. Amino acids—Cysteine, NAC, L-glutamine, Glutathione

Many studies and a lot of research are happening now on healing autoimmune conditions with diet and lifestyle.  Doctors like Sarah Ballantyne and Terry Wahls are using diet and lifestyle to control autoimmune disease symptoms without the use of immune-suppressing drugs.  Instead, they have focused on sealing the gut, helping the gut microbiome flourish, and eating to support the immune system and help the entire body function as well as possible.  Dr. Terry Wahls has successfully used these methods to reverse most of the damage done by her MS.  Once in a tilt-recline wheelchair, she now bikes, jogs, and runs clinical trials on her methods as well as running a clinic for the VA.  Autoimmunity cannot, at least yet, be switched off, but it can be greatly managed and perhaps halted with diet and lifestyle.  For detailed information on how to treat autoimmunity with diet and lifestyle, see The Wahls Protocol by Dr. Terry Wahls and The Paleo Approach by Dr. Sarah Ballantyne.

While lifestyle factors are not to be overlooked, nutrition is crucial and my focus here.  Poor nutrition is a large part of what gets us into the dysbiosis-LGS-autoimmune cycle, but good nutrition can also help us seal the gut and get it working well again.  Dysbiosis is triggered, to a great degree, by poor nutrition. Then, the dysbiosis itself makes good nutrition even harder to attain.  A healthy, balanced microbiome helps to digest and assimilate the nutrients needed.  LGS means that the cells charged with transporting needed nutrients into the body are not functioning properly.  So, we find ourselves more and more malnourished.  Very often this malnourishment takes the form of micronutrient and healthy fat deficiency.  This further sets the stage for autoimmunity as the immune system is starved of the micronutrients, amino acids, and essential fatty acids it needs to function properly. (Ballantyne, 2014)

Let’s take a deeper look at three key nutrients:

Vitamin C:  A key antioxidant and a regulator of the immune system.  Vitamin C defends intestinal cells from oxidative damage.  In addition, Vitamin C is required for the body to produce collagen.  Collagen is an integral protein throughout the body that provides structure for tissues, including the intestines. (Murray, 2005)

Foods highest in Vitamin C are peppers, guava, kale (best but other greens high), broccoli and other brassicas, red cabbage, strawberries, spinach, oranges and other citrus fruits.  (Murray, 2005)

Zinc:  Zinc is a mineral crucial to proper immune function.  Marginal deficiency in the United States is common. (Murray, 2005) Zinc is also vital for maintaining the integrity of the intestinal wall.  Even 8 weeks, zinc supplementation can show huge gains in intestinal permeability. (Defelice, 2005) Research has proven zinc helps heal leaky gut in patients with Crohn’s Disease and that zinc is very commonly deficient in those with LGS. (Hogg, 2015)

The RDA is 15 mg for men and 12 mg for women.  Therapeutic doses for healing LGS are 50-80 mg per day, not to exceed 100 mg daily.  Above 100mg daily, zinc actually depresses immune function. It is helpful to balance zinc with copper, taking 1mg for every 15 mg of zinc supplementation.  (Hogg, 2015)

Best dietary sources of zinc are oysters, pumpkin seeds, ginger root, pecans, brazil nuts, legumes, and grains (although these last two are not recommended on an LGS healing diet.) (Murray, 2015) Zinc is less bioavailable in plant foods, making animal sources more useful. (Bauman, 2015)

L-glutamine: L-glutamine (also known as glutamine) is an amino acid present in many protein-rich foods.  It is the most abundant amino acid found in the body and is involved in more metabolic processes than any other. (Murray, 2015)  L-glutamine is also the best compound known for improving LGS.  Enterocytes in the small intestine and GALT cells both use L-glutamine as fuel.  Because of its rapid uptake by our immune system, those with LGS and an up-regulated immune system, need larger amounts of L-glutamine.

L-glutamine levels in foods are not labeled or easy to track.  The L-glutamine in animal sources is higher and more bioavailable.  Making bone broth, a traditionally prepared, long-simmered stock from bones, is a great way to boost L-glutamine levels naturally.

In the case of LGS and autoimmunity, supplementation is strongly encouraged.  What the body cannot use will be eliminated and recommendations for supplementation vary widely—from 2-5 grams daily (Bauman, 2015) to 10-40 grams daily (Ballantyne, 2014.)  It is best to take it on an empty stomach for maximum absorption.  L-glutamine is a crucial part of the Repair phase in the 4R gut healing protocol.

Other Recommendations for Synergistic Foods, Nutrients, and Herbs:

Probiotics: Probiotics are healthy bacteria that populate our digestive tract that our immune systems need to function properly.  We know that there is a strong link between dysbiosis and LGS.  Healing dysbiosis is a large part of healing intestinal permeability.  Probiotics not only help repopulate the gut with healthy microbiota but also can help seal those leaky tight junctions between enterocytes. (Ballantyne, 2015) We can consume probiotics in the form of fermented foods as well as by supplementation.  Examples of safe anti-allergenic fermented foods include raw, unpasteurized lacto-fermented vegetables like sauerkraut, carrots, and pickles; kombucha; water and coconut water kefir, and homemade coconut yogurt.  Avoid commercial yogurts that beyond being made from gut-irritating dairy, are very processed, loaded with sugar, and contain a limited amount of helpful probiotics.  Try to eat at least ¼ cup of probiotic-rich foods daily.

Probiotic supplementation, especially during the Reinoculation phase of the 4R protocol, is very useful.   Again, recommendations for formulas and amounts vary widely.  Stool analysis is available that allows you to know what strains are flourishing in your gut and help you target certain strains in supplementation.  Remember, there are thousands of different species.  Lactobacillus and Bifidobacterium are key microbes to include in supplementation.  A good approach is to take at least 35 billion organisms a day for four weeks and then reduce to 10 billion organisms a day for another month. (Jade, 2015)

Researchers agree that variety is important. One way to introduce a wide variety of probiotics into your diet is to look at soil-based organisms.  Getting your own hands into the soil to grow and harvest that food is even better.  We live in a hyper-sterile culture.  Food fresh from the farm with a little dirt may be a great probiotic prescription. (Miller, 2015)

Butyric Acid:  This is a SCFA (short chain fatty acid) that is produced naturally by gut microbes in the large intestine as they digest fiber.  This fatty acid serves as fuel for the cells lining the large intestine.  When dysbiosis and LGS are present, dietary measures and supplementation can boost butyric acid. (Bauman, 2015) Eating a high fiber diet boosts butyric acid if you have the right gut microbes present.  Dairy products have butyric acid but are to be avoided for gut health.  If you have eliminated them and successfully reintroduced dairy products like ghee or raw cultured dairy, they could help supply butyric acid. Supplementation can help healing.  600-1200 mg three times daily with meals is the recommended therapeutic dose. (Jade, 2015)

Digestive Enzymes:  These target the Replace phase of the 4R protocol.  Low levels of hydrochloric acid in the stomach and digestive enzymes can be a cause of and common contributing factor to LGS. (Jade, 2015) Digestive bitters from foods like dandelion, lemon juice, and apple cider vinegar are a natural way to boost hydrochloric acid, digestive enzymes, bile production, liver function, and more. (Grossman, 2014)

To evaluate your need for a hydrochloric acid booster, follow a protocol like the one outlined at the American Nutrition Association website (see references for full web address.) The need for and amount of supplementation needed for digestive enzymes can also be gained from stool analysis.  Digestive enzymes help an overworked and healing intestinal tract.  A well-rounded enzyme supplement should contain: Protease – breaks down proteins, Amylase – breaks down starches, Lipase – breaks down fats and Lactase – breaks down lactose in dairy (if consuming.)

Gelatin and Collagen: Collagen makes up 30% of our bodies—giving structure to skin, hair, nails, bones and more.  Gelatin is the cooked version of collagen.  It’s a protein made of a group of amino acids—in particular, amino acids like proline and glycine which help rebuild the intestinal lining and support the health of the intestinal mucosal layer. (Axe, 2015) They also contain glutamic acid that our body converts into L-glutamine for further intestinal healing.  I recommend the Vital Proteins brand Collagen Peptides and Gelatin.  They are sourced from grass-fed beef.   The Collagen Peptides is a cold water soluble supplement that can be mixed in with drinks, oatmeal, etc.  The gelatin must be mixed with hot beverages or soups.  There are no official dosing guidelines, but mixing a scoop (about 20 grams) into a beverage morning and evening is a good guideline.  The gelatin is more satiating and is a good option for evenings.

Vitamin D:  Vitamin D is an important modulator of the immune system and has been proven to be crucial to maintaining intestinal mucosal and barrier integrity when infectious agents are in the microbiome.  Low Vitamin D levels are a causal factor in increased intestinal permeability.  (Assa, 2014)

Our bodies can make Vitamin D when we are exposed to sunlight. This is rarely enough to keep levels optimal.  Vitamin D can be obtained from foods such as cod liver oil, fatty fish, beef liver, oysters, eggs, and mushrooms. A Vitamin D level of 50-100 ng/ml is recommended.  (Wahls, 2014) You should have your blood levels tested and supplement as directed.  Supplementation is commonly needed so do not overlook being tested.

DGL: This is licorice root that has had the glycyrrhizin removed.  Glycyrrhizin is a compound that has been shown to cause edema and hypertension, but this deglycyrrhizinized version helps with LGS.  DGL supports the mucous lining of the stomach and upper small intestine.  DGL is an adaptogenic herb that helps regulate hormone levels. It helps in the absorption and metabolism of the hormone cortisol, thus battling adrenal fatigue and supporting gut health by helping modulate stress levels. (Axe, 2015)

DGL can be added to the diet as a powder, supplement, or tea.  500 mg twice daily is a good therapeutic dose.


American Nutrition Association (no date) Hydrochloric Acid Protocol. Available at: http://americannutritionassociation.org/toolsandresources/hydrochloricacidprotocol

Assa, A., Vong, L., Pinnell, L., Avitzur, N., Johnson-Henry, K. and Sherman, P. (2014) ‘Vitamin D deficiency promotes epithelial barrier dysfunction and intestinal inflammation’, The Journal of infectious diseases., 8(210) Available at: http://www.ncbi.nlm.nih.gov/pubmed/24755435

Axe (2015) Top 10 leaky gut supplements. Available at: http://draxe.com/leaky-gut-supplements/

Ballantyne, S. (2014) The Paleo Approach: Reverse Autoimmune Disease and Heal Your Body. United States: Victory Belt Publishing.

Bauman, E. (2015) Therapeutic Nutrition Textbook, Part 1. Penngrove, CA: Bauman College.

Defelice, Karen (2005) Enzymes & leaky gut/intestinal Permeability (2015) Available at: http://www.enzymestuff.com/conditionleakygut.htm

Grossmann, K. (2014) 10 reasons to use bitters (hint: It all starts with digestive health). Available at: http://blog.radiantlifecatalog.com/bid/70036/10-Reasons-to-Use-Bitters-hint-it-all-starts-with-digestive-health

Hogg, M. (2015) Leaky Gut Syndrome Treatment. Available at: http://www.ei-resource.org/treatment-options/treatment-information/leaky-gut-syndrome-treatment/

Hyman, M. (2010) How to stop attacking yourself.  Available at: http://drhyman.com/blog/2010/07/30/how-to-stop-attacking-yourself-9-steps-to-heal-autoimmune-disease/

Jade, K. (2015) Tired all the time? Try healing leaky gut syndrome for fatigue relief. Available at: http://www.naturalhealthadvisory.com/daily/fatigue-lack-of-energy/4-key-steps-to-healing-leaky-gut-syndrome-and-ending-your-%E2%80%9Ctired-all-the-time%E2%80%9D-feeling/

Liska, D., Bland, J. S., Lukaczer, D., Jones, D. S., Lerman, R. H., Bl, J. S., Costarella, L., Levin, B. and Schmidt, M. A. (2004) Clinical Nutrition: A Functional Approach. 2nd edn. Gig Harbor, WA: Institute for Functional Medicine.

Mercola (2008) Probiotics found to help your gut’s immune system. Available at: http://articles.mercola.com/sites/articles/archive/2008/07/05/probiotics-found-to-help-your-gut-s-immune-system.aspx

Mercola (2014) Which One works better: Antibacterial soap or plain soap? Available at: http://articles.mercola.com/sites/articles/archive/2015/09/29/antibacterial-soap.aspx

Mercola (2015) The importance of gut Microbiome for optimal health. Available at:  http://articles.mercola.com/sites/articles/archive/2015/07/13/importance-gut-microbiome.aspx

Miller, D. (2015) The surprising healing qualities … Of dirt. Available at: http://www.yesmagazine.org/issues/how-to-eat-like-our-lives-depend-on-it/how-dirt-heals-us

Murray, M., Pizzorno, L. and Pizzorno, J. N. D. (2005) The Encyclopedia of Healing Foods. United States: Atria Books.

Wahls, T. and Adamson, E. (2014) The Wahls Protocol: How I Beat Progressive MS Using Paleo Principles and Functional Medicine. New York, NY: Avery Publishing Group Inc., U.S.