top of page


Leaky gut syndrome


The gut barrier is paradoxical in that it must allow the passage of nutrients while keeping out offending antigenic substances and microorganisms in the gut. The gut is typically partly “leaky,” allowing particles as large as bacteria and entire undigested proteins to cross it, and it is normal to find gut bacteria in the portal blood, on the “wrong” side of the gut barrier. These and other antigens or pathogens are typically controlled by the extensive gut lymphatic material and by the liver. If gut permeability increases, however, large amounts of antigenic material can overwhelm these systems, and a cascade of inflammatory events may ensue that can trigger or exacerbate autoimmunity.

Leaky gut can result in vicious-cycle type pathologies. Gut inflammation can impair absorption of nutrients, and the resulting malnutrition can result in further reduction of the barrier integrity or an increase in inflammation.

The hyper permeable gut can allow food antigens across the barrier, initiating allergic reactions that further impair the gut integrity. Toxic overload on the liver’s antioxidant systems can likewise impair the liver’s ability to handle the overload.

The presence of a leaky gut syndrome associated with various illnesses, including autoimmunity, has been a theory of alternative medicine since the mid-1980s, but studies and trials that support the theory now abound in the scientific literature.

Research studies indicate that gut permeability may be pathologically increased by:

  • antibiotic therapy

  • non-steroidal anti-inflammatory drugs

  • food allergies

  • alcohol

  • stress, and

  • poor nutrition.

Research also shows that the gut does not increase in permeability due to normal aging, that mother’s milk can protect against permeability-inducing injuries, and that administration of probiotics and L-Glutamine can restore normal permeability,

Various researchers have also linked increased intestinal permeability with:

  • autoimmune diseases in general

  • arthritis

  • ankylosing spondylitis

  • collagen autoimmune diseases

  • Crohn’s Disease and Ulcerative colitis

  • and autoimmune skin disorders

  • Psychological changes & brain dysfunction

Two key lab tests that patients would need:

A urine test


A key factor in research into intestinal permeability has been the cellobiose/mannitol sugar permeability test, a simple lab test which assesses the absorption of sugars of high and low molecular weights across the intestinal barrier by measuring urine concentrations, we offer  The Organic Acids Test (OAT) offers a comprehensive metabolic snapshot of a patient’s overall health with over 70 markers. It provides an accurate evaluation of intestinal yeast and bacteria. Abnormally high levels of these microorganisms can cause or worsen behavior disorders, hyperactivity, movement disorders, fatigue and immune function. Many people with chronic illnesses and neurological disorders often excrete several abnormal organic acids in their urine. The cause of these high levels could include oral antibiotic use, high sugar diets, immune deficiencies, acquired infections, as well as genetic factors.


Gut functional test


The ability to digest and selectively absorb nutrients from our foods and beverages is one of the cornerstones of good health. To obtain benefits from food that is consumed, nutrients must be appropriately digested and then efficiently absorbed into portal circulation.
Microbes, larger sized particles of fibre, and undigested foodstuffs should remain within the intestinal lumen. Poor digestion and malabsorption of vital nutrients can contribute to problems with degenerative diseases, compromised immune status, and deficiency states caused by inadequate mineral, vitamin, carbohydrate, fats, and amino acids status.

In addition to digestion and selective absorption, the gastrointestinal tract eliminates undigested food residues and toxins that are excreted via the bile into the intestinal tract and provides a niche for the proliferation of friendly microorganisms.

Impairment of the selective absorptive capacity or of the barrier function of gut (as in “excessive intestinal permeability”) can result from a number of suspected causes. Common associated causes include: low stomach acid; chronic maldigestion; food allergens’ impacting on the bowel absorptive surfaces; bacterial overgrowth or imbalances (dysbiosis); pathogenic bacteria, yeast or parasites with related toxic irritants; and the use of NSAID’s and antibiotics.

Impairment in intestinal function can contribute to the development of food allergies, systemic illnesses, autoimmune disease, and toxic overload from substances which are usually kept in the confines of the bowel for elimination.

The Comprehensive Stool Analysis with Parasitology  identifies live bacteria and yeast, parasites, maldigestion, bacterial metabolism, inflammation and immune function. Important information regarding the efficiency of digestion and absorption can be gleaned from the measurement of the faecal levels of elastase (pancreatic exocrine sufficiency), muscle and vegetable fibers, carbohydrates, and total fat.

How to heal a leaky gut

Molecular mimicry

A second contemporary concept in autoimmunity may explain the devastating effects of compromise of the gut barrier. Molecular mimicry describes a condition in which protein sequences in bacteria, viruses, foods, or other antigens are similar or identical to sequences in human tissues. Thus antibodies to the mimicking substance may attack the corresponding tissue in the body. Molecular mimicry has long been recognized as the cause of autoimmune disease that appears in the aftermath of acute infections, but recent research demonstrates that the phenomenon is much more widespread than previously thought, and that antibodies to gut bacteria and undigested food proteins may also attack various human tissues. Molecular mimicry between the gut bacterium Klebsiella spp and the body’s tissues has been recognized as a probable causative factor in autoimmune ankylosing spondylitis at least since 1977. Antibodies to some of the materials flooding into the system through a leaky gut could thus trigger the onset or an exacerbation of autoimmunity.

Molecular mimicry and cross reactivity between gluten protein and human tissues has recently been documented. Gluten has long been known to produce celiac disease in some individuals. Celiac disease is accompanied by the autoimmune destruction of the intestinal wall as antibodies to gluten attack the epithelial cells of the intestine (Tuckova et al). It has recently been recognized that the antibodies to gluten may not significantly affect the intestine, but instead attack other tissues throughout the body. Kamaeva et all suggest that molecular mimicry of the gluten protein has been identified in:

  • autoimmune thyroid disease,

  • systemic lupus,

  • autoimmune nephritis,

  • psoriasis,

  • juvenile rheumatoid arthritis,

  • and other autoimmune  diseases.


Cross reactive anti-gluten antibodies were found in 19 of sixty patients with various autoimmune disease, including 4 of 16 cases of rheumatoid arthritis and 1 of 8 cases of systemic lupus evaluated in the study. The study implies that removal of gluten from the diet may improve these other conditions just as it does for celiac disease.

Milk protein has been implicated in similar pathologies, with one study finding a direct proportion between circulating autoandibodies and the antibody to the casein protein in cow’s milk. The researchers also found that 10% of the subjects they measured in the general population had cross reactive autoantibodies between cow’s milk protein and body tissues. Soy protein has also been implicated in autoimmune diseases, especially autoimmune thyroiditis

Other barriers

The gut barrier is not the only one implicated in autoimmune disease. Researchers have theorized that autoimmune pathologies may involve imperfections of  the blood-brain barrier, the blood-nerve barrier , the blood-retina barrier, the bladder epithelial barrier, the arterial-endothelial barrier, and the placental barrier.


The association between pregnancy and the onset of several autoimmune diseases, including SLE, is well-established. A mechanism called “microchimerism” may explain the phenomena. Microchimerism describes a condition in which fetal cells, including components of the immune system, can enter maternal blood and remain there, for decades sometimes. Maternal immune cells can also enter the  fetal blood, reproduce there, and linger into later life. Male fetal DNA has been found in mother’s blood as long as twenty-seven years after birth, and as many as 4% of the white blood cells in infants have been found to have originated in the mother’s blood. White blood cells may remain in the foreign blood, replicating and producing antibodies, for long periods of time. Both situations are implicated by association with autoimmune disease such as scleroderma and lupus.

The pathologies described above may explain why autoimmunity is a modern disease, and rarely seen in primitive societies following traditional dietary and lifestyle patterns. The malnutrition in key vitamins and minerals common with the modern diet may injure barrier integrity.

Modern anti-inflammatory drugs, available over-the-counter and widely consumed either through medical prescription or self-medication, as well as other prescription drugs, may induce leaky gut.


In general, conventional medicine can do little for autoimmunity other than turning off the inflammatory mechanisms with drugs.

This may be important in life threatening situations, but,  if  leaky gut and accompanying molecular mimicry are not corrected, the disease can be expected to progress, now complicated by drug side effects. Ironically, some of the drugs used to treat autoimmune diseases themselves can produce leaky gut syndrome.

Implications for natural medicine (functional medicine)

Natural medicine, on the other hand, may present possibilities for preventing and treating the underlying pathologies. The following strategies might be considered in any case of autoimmunity.

  1. Maintain or restore barrier integrity through optimal nutrition.

  2. Balance fats and oils in the diet to promote sufficient levels and balance in the anti-inflammatory prostaglandins.

  3. Withdraw and/or avoid non-essential pharmaceutical drugs that can induce leaky gut, especially antibiotics, non-steroidal anti-inflammatory drugs, and corticosteroids.

  4. Screen for and eliminate food allergens.

  5. Recommend avoidance of alcohol or treatment for alcoholism

  6. Counsel or make referrals for stress reduction. Consider spa therapy for rest during acute attacks.

  7. Prescribe gut-healing anti-inflammatory, demulcent, and/or carminative herbs.

One consideration when seeking to apply the principles of traditional herbal systems such as traditional Chinese medicine, Ayurveda, or Unani Tibb is to bear in mind that autoimmunity itself is a disease of modern society, especially of the twentieth century.

Leaky gut syndrome and the related issues above were probably rare as the above systems were being developed, and preexisting protocols do  not exist in those systems for autoimmune diseases.

Assessment of the clinical picture and the history for the development of and presence of leaky gut syndrome, and treatments to reduce gut permeability might be prudent first steps to take in the treatment of autoimmunity, regardless of the traditional system being used.


This is life-altering material for you and your family. Begin to explore some of what is presented here and learn everything you can. It is, after all, your body, health and life, every day. Remember that it is potentially dangerous to follow some of the stricter dietary approaches and protocols you may uncover, so we always strongly encourage you to work directly with a credentialed clinician as part of your healing journey.

9 steps to treating autoimmune disease

  1. Check for hidden infections — yeast, viruses, bacteria, SIBO, Lyme, etc. — with the help of a doctor, and treat them. (we do Genova Dx urine and stool analysis)

  2. Check for hidden food allergens with IgG food testing or just try The Leaky Gut Diet, which is designed to eliminate most food allergens. (we do this Cyrex Labs blood test)

  3. Get tested for celiac disease, which is a blood test that any doctor can do.

  4. Get checked for heavy metal toxicity. Mercury and other metals can cause autoimmunity. (we do this Cyrex Labs blood test)

  5. Fix your gut. For details, see this blog on irritable bowel syndrome.

  6. Use nutrients such as fish oil, vitamin C, vitamin D, and probiotics Providing the nutrients necessary to help the gut repair itself is essential. One of my favorite supplements is L-glutamine, an amino acid that helps to rejuvenate the gut wall lining. Other key nutrients include zinc, omega-3fish oils, anti-oxidants and herbs such as deglycyrrhizinated licorice (DGL) and aloe vera. to help calm your immune response naturally.

  7. Exercise regularly — it’s a natural anti-inflammatory.

  8. Practice deep relaxation like yoga, deep breathing, biofeedback, or massage, because stress worsens the immune response.

  9. Tell your doctor about Functional Medicine (it is different from Allopathic Medicine) encourage them to support your journey back to health— go to for more information and to get a copy of the Brian Health Book


​Bjarnason I, Peters TJ, Wise RJ.The leaky gut of alcoholism: possible route of entry for toxic compounds. Lancet. 1984 Jan 28; 1(8370): 179-182. Bijlsma PB, Peeters RA, Groot JA, Dekker PR, et al. Differential in vivo and in vitro intestinal permeability to lactulose and mannitol in animals and humans: a hypothesis. Gastroenterology 1995 Mar;108(3):687-96 Brosnan CF, Claudio L, Tansey FA, Martiney J. Mechanisms of autoimmune neuropathies. Ann Neurol 1990;27 Suppl:S75-S79 Bullock AD, Becich MJ, Klutke CG, Ratliff TL. Experimental autoimmune cystitis: a potential murine model for ulcerative interstitial cystitis. J Urol 1992 Dec;148(6):1951-1956 Claudio L, et al. Evidence of persistent  blood-brain barrier abnormalities in chronic-progressive multiple sclerosis. Acta Neuropathol (Berl). 1995; 90(3): 228-238. Claudio L, et al. Ultrastructural studies of the blood-retina barrier after exposure to interleukin-1 beta or tumor necrosis factor-alpha. Urol Clin North Am 1994 Feb;21(1):31-39 Crissinger KD and Burney DL Intestinal oxygenation and mucosal permeability with luminal mother’s milk in developing piglets. Pediatr Res 1996 Aug;40(2):269-75 Cunningham-Rundles C, Feng ZK, Zhou Z, Woods KR. Relationship between naturally occurring human antibodies to casein and autologous antiidiotypic antibodies: implications for the network theory. J Clin Immunol 1991 Sep;11(5):279-290 de Boissieu D, Dupont C, and Badoual J. Allergy to nondairy proteins in mother’s milk as assessed by intestinal permeability tests. Allergy 1994 Dec;49(10):882-4 Ebringer R, Cooke D, Cawdell DR, Cowling P, Ebringer A. Ankylosing spondylitis: klebsiella and HL-A B27. Rheumatol Rehabil 1977 Aug;16(3):190-196 Fort P, Moses N, Fasano M, Goldberg T, Lifshitz F.  Breast and soy-formula feedings in early infancy and the prevalence of autoimmune thyroid disease in children. J Am Coll Nutr 1990 Apr;9(2):164-167 Fort P, Lanes R, Dahlem S, Recker B, Weyman-Daum M, Pugliese M, Lifshitz F.  Breast feeding and insulin-dependent diabetes mellitus in children. J Am Coll Nutr 1986;5(5):439-441 Galland, L. The Four Pillars of Healing : How Integrated  Medicine Can Heal You. New York: Random House, 1997 Galland L. Leaky Gut Syndromes: Breaking the Vicious Cycle. Http:// Geboes K  From inflammation to lesion. Acta Gastroenterol Belg 1994 Sep;57(5-6):273-284 Jenkins AP, trew DR, Crump BJ, et al Do non-steroidal anti-inflammatory drugs increase colonic permeability? 1991; Gut 32:66-69 Kamaeva OI, Reznikov IuP, Pimenova NS, Dobritsyna LV. Antigliadin antibodies in the absence of celiac disease. Klin Med (Mosk) 1998;76(2):33-35 Karlsen AE, Dyrberg T. Molecular mimicry between non-self, modified self and self in autoimmunity. Semin Immunol 1998 Feb;10(1):25-34 Kieffer M, Barnetson RS  Increased gliadin antibodies in dermatitis herpetiformis and pemphigoid. Br J Dermatol 1983 Jun;108(6):673-678 Louis E, Franchimont D, Deprez M, Lamproye A, et al. Decrease in systemic tolerance to fed ovalbumin in indomethacin-treated mice. Int Arch Allergy Immunol 1996  Jan;109(1):21-6 Ma TY. Intestinal epithelial barrier dysfunction in Crohn’s disease. Proc Soc Exp Biol Med 1997 Apr;214(4):318-27 Martinez-Gonzales et al. Intestinal permeability in patients with ankylosing spondylitis and their healthy relatives. Br J Rheumatology 1994;33:644-647 Neal DE Jr, Dilworth JP, Kaack MB. Tamm-Horsfall autoantibodies in interstitial cystitis. J Urol 1991 Jan;145(1):37-39 Nelson JL. Microchimerism and Autoimmune Disease NEJM 1998;338(17). Nylander O, Andersson H, Wilander E, and Sababi M. Prostaglandins reduce hydrochloric acid-induced increase in duodenal mucosal permeability by a mechanism not related to stimulation of alkaline secretion. Paganelli R, et al. Intestinal permeability in patients with chronic urticaria-angioedema with and without arthralgia. Ann Allergy 1991;66:181-184 Parke AL. Gastrointestinal disorders and rheumatic diseases. Curr Opin Rheumatol 1991 Feb;3(1):160-165 Pizzorno, J. Total Wellness. Rocklin, California: Prima Publishing, 1997 Rodriguez P, Darmon N, Chappuis P,Candalh C, et al. Intestinal paracellular permeability during malnutrition in guinea pigs: effect of high dietary zinc. Gut 1996 Sep;39(3):416-22 Rutgers HC, Batt RM, Proud FJ, Sorensen SH, et al. Intestinal permeability and function in dogs with small      intestinal bacterial overgrowth. J Small Anim Pract 1996 Sep;37(9):428-34 Salminen S, Isolauri E, Salminen E. Clinical uses of probiotics for stabilizing the gut mucosal barrier: successful strains and future challenges. REVIEW ARTICLE: 90  REFS. Antonie Van Leeuwenhoek 1996 Oct;70(2-4):347-58 Saltzman JR, Kowdley KV, Perrone G, and Russell RM Changes in small-intestine permeability with aging. J Am Geriatr Soc 1995 Feb;43(2):160-4 Saunders PR, Kosecka U, McKay DM, and Perdue MH. Acute stressors stimulate ion secretion and increase epithelial permeability in rat intestine. Am J Physiol 1994 Nov;267(5 Pt 1):G794-9 Stevens TR, Winrow VR, Blake DR, Rampton DS. Circulating antibodies to heat-shock protein 60 in Crohn’s disease and ulcerative colitis. Clin Exp Immunol 1992 Nov;90(2):271-274 Troncone R, et al. Increased intestinal sugar permeability after challegne in children with cow’s milk allergy or intolerance. Allergy 1994:49:142-146 Troncone R, Mayer M, Mugione P, Cucciardi M, et al. Cellobiose/mannitol sugar permeability test in children in relation to jejunal morphometry. Ital J Gastroenterol  1995 Dec;27(9):489-93 Tsutsumi A, Sugiyama T, Matsumura R, Sueishi M, Takabayashi K, Koike T, Tomioka H, Yoshida S.  Protein losing enteropathy associated with collagen diseases. Ann Rheum Dis 1991 Mar;50(3):178-181 Tuckova L, Karska K, Walters JR, Michalak M, Rossmann P, Krupickova S, Verdu EF, Saalman R, Hanson LA, Tlaskalova-Hogenova H.  Anti-gliadin antibodies in patients with celiac disease cross-react with enterocytes and human calreticulin.  Clin Immunol Immunopathol 1997 Dec;85(3):289-296 Wallace JL. Pathogenesis of nonsteroidal anti-inflammatory drug gastropathy: recent advances. Eur J Gastro Hepatol 1993;5:403-407 Whang EE, Dunn JC, Mahanty H, McFadden DW, et al. Endotoxin inhibitor prevents sepsis-induced alterations in intestinal ion transport. Am J Surg 1996 Oct;172(4):341-4 Wissler RW  Update on the pathogenesis of atherosclerosis. Am J Med 1991 Jul 31;91(1B):3S-9S Yu RK, Ariga T, Kohriyama T, Kusunoki S, Maeda Y, Miyatani N. Autoimmune mechanisms in peripheral neuropathies. Ann Neurol 1990;27 Suppl:S30-S35

bottom of page