Bad Guys in the Gut: Overcoming Autoimmunity

Increased Intestinal Permeability (Also known as “Leaky Gut”)

In Hashimoto’s thyroiditis, we see gradual physical and functional deterioration of the thyroid gland. If the thyroid gland isn’t functioning properly, normal physiologic function cannot easily occur.  This means all cells throughout the body are not functioning properly. Symptoms associated with Hashimoto’s include:

An autoimmune disorder like Hashimoto’s is a response to some environmental trigger in a genetically susceptible individual in the presence of increased intestinal permeability. How can your gut simply become porous and let things pass through when it previously blocked those same (now harmful) entities?

Our intestinal tissue can become "leaky" when the myriad of factors that maintain structural integrity break down. This could be due to poor diet and lifestyle choices or it could also be due to an environmental exposure like the pesticide RoundUp or to genetically-modified crops (GMO).

Some of the biggest culprits to start this chain of reactions are GMO crops (i.e., wheat, corn, soy) and dairy products.  Since 1996 Roundup ready GMO crops were introduced into agriculture and have been grown at exponential rates since. It has been known for decades both GMO crops and Roundup are carcinogenic since they kill all cell function in both plants, animals, and humans.  These crops are primarily used for animal feed, to make beer, most processed ready-made food, bread, and other wheat, corn, and soy products. 

The molecular structure of many GMO crops (especially wheat) and casein (in dairy products) "looks" very similar to the thyroid gland’s protein structure.  In an attempt to prevent you from harm, the immune system neutralizes the threat from these unsafe proteins since they should not be in our bloodstream. In the process of creating antibodies against these unsafe foods and attacking them, the immune system also begins accidentally attacking the thyroid gland since its protein structure appears similar to the foreign protein.  Autoimmunity is now born (aka., your own immune system begins attacking you). 

As the case of "mistaken identity" continues (again, due to consuming the same food that initiated the damage), the immune system becomes destructive in its attack of thyroid tissue. This variety of autoimmune disease may present as Hashimoto's thyroiditis in some, versus as type I diabetes, multiple sclerosis, celiac disease, Crohn’s disease, rheumatoid arthritis, lupus, or cancer in someone else. 


Intestinal Dysbiosis

An area that is greatly affected by gastrointestinal dysbiosis (also known as microbial imbalance, i.e. an overgrowth of “bad bugs” and insufficient growth of “good bugs” in the gut) is the thyroid gland. Lacking beneficial strains of bacteria or having an overgrowth of harmful ones in the gut has been clearly linked to autoimmune thyroid disease (Kohling et al., 2017). The microbiome of individuals with Hashimoto’s versus healthy controls have bacterial overgrowth (Ishaq et al., 2017). While further research is required, approaching autoimmunity from a different lens can give us an idea about what else is happening in the gut.

Let’s focus on gram negative bacteria. These are considered to be the “Bad Guys” when they grow out of control.

A byproduct of gram negative bacteria is an endotoxin called lipopolysaccharide (LPS). When LPS is released into the bloodstream from intestinal tissue, it causes thyroid mast cell degranulation (Yaglova and Yaglov, 2013). When mast cells degranulate, they release several inflammatory mediators which bombarded the thyroid gland. Inflammation continues to spike when LPS also appears and hence, creates a warzone.  

With Hashimoto's and most autoimmune diseases, I begin by working on the major component of the disease: inflammation. Treatment would be focused on five areas:

  1. Optimizing hydration and allowing the immune system to rest (via intermittent fasting).
  2. Consuming anti-inflammatory alkaline plant-based foods, herbs, and spices such as turmeric and green tea to help reduce inflammatory markers.  Consider licorice root and Ashwagandha to help improve digestive function, hormone levels, and thyroid function.
  3. Ensuring proper rest and relaxation. You NEED sleep to repair and heal.
  4. Shift to a GMO-free diet because many patients with autoimmune disease usually have more than one autoimmune disorder. Because we know cross-reactivity occurs, avoidance of GMO crops (i.e., wheat, corn, soy; animal proteins fed GMO crops, processed pre-packaged ready-made food) and dairy products is paramount. We don't want the body to mistake these foreign proteins for other bodily tissues.


Patient Testimonial

“I did find that healing my gut played a major role in cooling down the autoimmune reaction and inflammation. I did IgG testing and removed eggs, gluten, dairy, and yeast. In reducing the massive amount of inflammation in my system and supplementing with glutamine-containing products, I was able to allow my intestinal permeability to heal. With a modified diet, I am no longer on thyroid medicines and feel great. While the autoimmune portion will always be present with the TPO antibodies that can fluctuate up and down, I know I have control over keeping down inflammation and allowing symptoms to disappear. Amazing how powerful the proper information can be.”  ~ JJ


Dr. Bhandari M.D. and the Advanced Health Team Are Here to Support Your Health


Dr. Bhandari and the Advanced Health team of experts work to help patients with Hashimoto’s thyroiditis and other chronic autoimmune disorders. They’re always ready to share their expertise on this commonly misunderstood disease. To book an appointment, contact Advanced Health or call 1-415-506-9393.




Cindoruk, M., Tuncer, C., Dursun, A., Yetkin, I., Karakan, T., Cakir, N., & Soykan, I. (2002). Increased colonic intraepithelial lymphocytes in patients with Hashimoto's thyroiditis. Journal of Clinical Gastroenterology, 34, 237-239.

Ishaq, H. M., Mohammad, I. S., Guo, H., Shahzad, M., Hou, Y. J., Ma, C., ... Xu, J. (2017). Molecular estimation of alteration in intestinal microbial composition in Hashimoto's thyroiditis patients. Biomedicine & Pharmacotherapy, 95, 865-874.

Köhling, H. L., Plummer, S. F., Marchesi, J. R., Davidge, K. S., & Ludgate, M. (2017). The microbiota and autoimmunity: Their role in thyroid autoimmune diseases. Clinical Immunology183, 63-74. 

Xu, M., Iwasaki, T., Shimokawa, N., Sajdel-Sulkowska, E. M., & Koibuchi, N. (2013). The effect of low dose lipopolysaccharide on thyroid hormone-regulated actin cytoskeleton modulation and type 2 iodothyronine deiodinase activity in astrocytes. Endocrine journal60(11), 1221-1230. 

Virili, C., Bassostti, G., Santaguida, M. G., Iuorio, R., Del Duca, S. C., Mercuri, V., ... Centanni, M. (2012, January 11). Atypical celiac disease as cause of increased need for thyroxine: a systematic study. Journal of Clinical Endocrinology and Metabolism, 97, E419-422.

Yaglova, N. V., & Yaglov, V. V. (2013). Ultrastructural characteristics of molecular release of secretory products from thyroid mast cells induced by lipopolysaccharide. Bulletin of experimental biology and medicine155(2), 260.

Payal Bhandari M.D. Dr. Payal Bhandari M.D. Dr. Payal Bhandari M.D. is one of U.S.'s top leading integrative functional medical physicians and the founder of San Francisco' top ranked medical center, SF Advanced Health. Her well-experienced holistic healthcare team collaborates together to deliver whole-person personalized care and combines the best in Western and Eastern medicine. By being an expert of cell function, Dr. Bhandari defines the root cause of illness and is able to subside any disease within weeks to months. She specializes in cancer prevention and reversal, digestive & autoimmune disorders. Dr. Bhandari received her Bachelor of Arts degree in biology in 1997 and Doctor of Medicine degree in 2001 from West Virginia University. She the completed her Family Medicine residency in 2004 from the University of Massachusetts and joined a family medicine practice in 2005 which was eventually nationally recognized as San Francisco’s 1st patient-centered medical home. To learn more, go to

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