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Bad Guys in the Gut: Overcoming Autoimmunity

It is well known that the gut is strongly connected to other bodily organs. Increased intestinal permeability (“leaky gut”) and dysbiosis can cause a myriad of health complaints beyond the gut, and this will be what I focus on at SF Advanced Health’s upcoming seminar on October 16th at 6:30 p.m.

Autoimmunity can loosely refer to any autoimmune state (Hashimoto’s, type I diabetes, multiple sclerosis, celiac disease, rheumatoid arthritis, cancer, etc.) since the underlying biologic principles are similar. For concrete clarity, I will be addressing autoimmunity with respect to Hashimoto’s thyroiditis in this blog.


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?

Because the environmental inputs have drastically changed.

It may not seem like common sense, but from your mouth to your stomach, small and large intestines, and then to your anus, your digestive tract is in constant contact with the outside world. In fact, in order for us to survive, we need to bring the outside world (food, water, air) to our inside world. It’s this interface between our outer and inner world that allows our bodies to take in the nutrients required to function and thrive. 

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).

Regardless of the specific (or multiple) triggering agents, the end result is the same proteins from the foods we eat do not completely break down into their smallest amino acids.  When these poorly digested foods come into direct contact with our immune system, they are viewed as foreigners by our body. Our immune system initiates a cascade of reactions to get rid of this foreigner.  This leads to inflammation throughout our body. 

Since we do not always recognize the foods we had originally believed to be safe are now the actual problem, we continue to maintain the same diet and  become increasingly disconnected by our eating habits and how they make us actually feel. Our cells become increasingly malnourished. Our digestive tract becomes increasingly damaged by the frequent attacks from the immune system.  Our immune system becomes increasingly tired constantly fighting off the “foreign” food. The damaged porous intestinal tract causes toxins to leak out into the bloodstream. Systemic inflammation (a.ka., the root cause of all chronic disease) now remains persistent.

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.  

The endotoxin LPS likely induces thyroid abnormalities morphologically and biochemically. This is via the disruption of thyroid hormones T4 and T3 functions like protein expression, growth factor release mediation, and actin polymerization. Disruption of this gland affects the central nervous system, and therefore brain cognition and memory formation (Xu et al., 2013). 

This should remind us how all of our organs are connected. Having a healthy microbiome is one solution for many, if not all, autoimmune diseases. 

Need more proof? It’s been found that ~40% of Hashimoto’s patients have histologic findings consistent with lymphocytic colitis, but were clinically (and surprisingly) asymptomatic (Cindoruk et al., 2002). Lymphocytic colitis is clearly associated with other autoimmune disorders (Cindoruk et al., 2002). Dosing requirements for the thyroid medication Levothyroxine are 50% higher in patients with concomitant celiac disease or Crohns’ disease since their gut microbiome is out of whack (Virili et al., 2012).

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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