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Gut Bacteria and Autoimmunity

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We are just beginning to gain an understanding as to the mechanisms underlying the role of gluten in inducing autoimmune diseases like type I diabetes. Much of our understanding stems from the landmark publication by Harvard’s Dr Alessio Fasano in which he provided and in-depth and comprehensive understanding of the role of the intestinal barrier in terms of regulating inflammation as well as autoimmunity. Fundamental to his thesis is the effect of gliadin, a component of gluten, on the integrity of the gut wall.

What Dr Fasano demonstrated was how gliadin induces the mobilization of another protein, zonulin, and how zonulin then goes on to increase the permeability of the bowel.[1] It is this increase in permeability that is playing a pivotal role in challenging the immune system, and leading to inflammation as well as autoimmunity.

Subsequent to Dr Fasano’s publication, researchers at the Mayo Clinic in Rochester Minnesota published exciting research that demonstrated a dramatic reduction in development of type I diabetes in laboratory mice if they were raised on a gluten-free diet.[2] While it is reasonable to assume that the preservation of gut integrity by not challenging it with gluten may have been responsible, the authors explored another intriguing possibility. What they found was that when these animals were placed on a gluten-free diet there was actually a significant change in the various species of gut bacteria in the animals tested.

Their conclusion stated:

Our novel study does suggest that dietary gluten could modulate the incidence of type I diabetes by changing the microbiome.

This is a very intriguing bit of information, as it correlates an autoimmune condition (type I diabetes) with changes in the gut bacteria.

We are now seeing a fairly dramatic increase in the incidence of various autoimmune conditions, including type I diabetes, rheumatoid arthritis, and systemic lupus erythematosus. This new research suggests that, if changes in gut bacteria pave the way for autoimmunity, then we have to ask ourselves, what environmental changes are bringing this about?

The human microbiome is sensitive to a variety of environmental factors including food choices, antibiotic usage, other medications, including nonsteroidal anti-inflammatory drugs, and even exposure to glyphosate, an herbicide now almost ubiquitous in agricultural products. The point is, when we alter the balance of bacteria that live within us, we set the stage for our most dreaded diseases, many of which did not have readily available pharmaceutical fixes.


  1. Fasano A. Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer. Physiol Rev 2011;91(1):151-175. [Full text]
  2. Marietta EV, Gomez AM, Yeoman C, et al. Low incidence of spontaneous type 1 diabetes in non-obese diabetic mice raised on gluten-free diets is associated with changes in the intestinal microbiome. PLoS One 2013;8(11):e78687. [Full text]

PUBLISHED WITH PERMISSION from Dr David Perlmutter. Original article may be found here


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Dr David Perlmutter - The Empowering Neurologist
Dr. Perlmutter is a Board-Certified Neurologist and Fellow of the American College of Nutrition who received his M.D. degree from the University of Miami School of Medicine where he was awarded the Leonard G. Rowntree Research Award. He has published extensively in peer-reviewed scientific journals including Archives of Neurology, Neurosurgery, and The Journal of Applied Nutrition, and is a frequent lecturer at symposia sponsored by such medical institutions as Columbia University, Scripps Institute, New York University, and Harvard University. He serves as Associate Professor at the University of Miami Miller School of Medicine. Dr. Perlmutter has been interviewed on many nationally syndicated television programs including 20/20, Larry King Live, CNN, Fox News, Fox and Friends, The Today Show, Oprah, The Dr.Oz Show and The CBS Early Show. He is the recipient of the Linus Pauling Award for his innovative approaches to neurological disorders and in addition was awarded the Denham Harmon Award for his pioneering work in the application of free radical science to clinical medicine. He is the recipient of the 2006 National Nutritional Foods Association Clinician of the Year Award and was awarded the Humanitarian of the Year award from the American College of Nutrition in, 2010. Dr. Perlmutter is the author of seven books including the #1 New York Times Bestseller, Grain Brain, The Surprising Truth About Wheat, Carbs and Sugar - Your Brain’s Silent Killers, now published in 27 countries. His new book, Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain–for Life, is now available nationwide and is a New York Times Bestseller.