Dysbiosis and Thyroid Dysfunction. All Roads Lead To The Microbiome.

Dysbiosis and Thyroid Dysfunction. All Roads Lead to the Microbriome.

There are trillions of bacteria in your gut that play a vital role in thyroid health, yet the microbiome is so often overlooked in the treatment of hypothyroidism.

Written by Raphael Kellman, M.D.

Thyroid disease and the microbiome are intricately intertwined and imbalances can set off a cyclical reaction. Low thyroid function can lead to inflammation and poor gut health while disturbances in the microbiome can suppress thyroid function and lead to an autoimmune condition called Hashimoto’s Thyroiditis.

In my practice the emphasis is always on healing the gut (intestines) and balancing the colonies of bacteria that live there called the microbiome. Trillions of bacteria live on us and in us with the largest concentration located in the intestine where 70% of our immune system also lives.

In practical terms, when the bacteria that make up our microbiome are healthy and thriving, so are we. Dysbiosis, or imbalances and overgrowth of unfriendly strains of bacteria can throw things off contributing to health and immune issues.

Likewise our actions impact the bacteria. Over-medicating with antibiotics and antacids destroys microbial populations. Environmental toxins, pesticides, heavy metal exposure, and chemicals in beauty and cleaning supplies also take a toll. Poor diets of sugary foods, refined carbs, GMO’s, gluten, and additives cause pathogenic strains to bloom. In the end the one who suffers is you.

How does the microbiome affect the thyroid?

Negative shifts in microbial populations can affect thyroid function, even triggering autoimmune disease.  

1) The majority of hormone produced by the thyroid is actually inactive T4, which needs to be converted to T3 before being used by cells. 20% of that hormone gets converted or activated in the intestine with the help of gut bacteria. Negative shifts in microbial populations will impact the amount of usable hormone that’s available, leading to a low thyroid state.

2) A major role of friendly gut bacteria is to strengthen the intestine wall, fortifying it against pathogens and preventing leaky gut. Without that barrier, foreign matter and large particles of food leak out of the intestine into the body setting off an immune response. Prolonged heightened immune response can trigger antibody production against healthy tissue creating autoimmune conditions like Hashimoto’s thyroiditis – the number one cause of low thyroid in America today.

3) When the microbiome is unbalanced, long-term inflammation and damage may ensue causing the adrenal glands to produce the stress hormone cortisol. Over time, too much cortisol can suppress thyroid function, lowering the amount of hormone produced while also inhibiting the conversion of T4 to T3.

4) H. Pylori is a pathogenic bacterium that colonizes areas of the stomach creating a wide range of digestive disorders including ulcers. Studies are now linking this bacterial infection to autoimmune conditions like Hashimoto’s (1).

How does the thyroid affect the microbiome?

If thyroid function is sluggish, all systems can slow down.

1) The main communication highway linking the brain and the intestine is called the vagus nerve. Commonly patients suffering with low thyroid also have a down-regulation in vagus nerve activity reducing the speed at which the intestines are working and processing food. When gut movement slows, constipation takes hold and food lingers in the small intestine.  This creates the ideal setting for pathogenic bacteria and candida to thrive and colonize. Patients often test positive for a condition called SIBO or small intestine bacterial overgrowth as a direct result of low thyroid. Symptoms are varied but may present as abdominal bloating and pain after meals, flatulence, constipation or diarrhea, heartburn, nausea, food sensitivities, headaches, fatigue, skin issues, and malabsorption.

2) Another consequence of low thyroid function is low stomach acid. While hydrochloric acid is our first line for protein breakdown, it also kills off bacteria hitching a ride on food. Without adequate HCL, proteins break down slower, nutrients aren’t absorbed as well and bacteria and yeast often make it into the intestine where they can take hold.  A lack of HCL has also been linked to increases in intestinal permeability and inflammation.

3) Since thyroid function affects the health of the intestine, the immune system is also affected. Dysbiosis will impact the way the immune system works making us more susceptible to infections, viruses, and parasites. Parasites steal our nutrients, create inflammation, damage tissues, and further upset the balance of the body.

4) Thyroid hormone also strengthens the joints or tight junctions between cells that make up the intestine wall. If the thyroid is underactive, tight junctions may become loose and leaky compromising intestinal health.

Bringing it all back into balance: The 4 R program to restore microbial and intestinal health.

Healing the gut and microbial communities will improve the overall health of the patient as well as boost the immune system. Typically I start by removing pathogens like fungus, parasites, yeast, and especially SIBO. Potent herbal compounds can break through biofilms making it easier to eradicate overgrowth. Berberine, wormwood, garlic, oregano oil, grapeseed and olive leaf extracts, and caprylic acid are very helpful.  I also use a clay/charcoal compound to assist with clearing toxins from die off.  Correcting the diet to support a healthy bacterial balance is also very important.  Additionally discontinuing unnecessary medications like PPI’s and avoiding overuse of antibiotics will protect our bacterial friends.  

Replace stomach acid and pancreatic enzymes to ensure foods are broken down and assimilated as well as kill unfriendly bacteria on foods.

Next we re-inoculate with probiotics and good flora. After eradicating the harmful strains, replenishing the good is very important. Targeted strains like S. Boulardii have an immune modulating effect either boosting or calming the immune system.

In this phase I always concentrate on prebiotic foods as well. The fibers found in superfoods like onion, garlic, jicama, asparagus, Jerusalem artichokes, leeks, radish, and tomato feed the beneficial bacteria and ensure they thrive. Fermented foods really pack a punch when it comes to replenishing the microbiome with large quantities of healthy bacteria while also including prebiotics.

Finally repair any damage to the intestinal wall, reducing inflammation and leaky gut. I use compounds like butyrate, quercetin, and curcumin to lower inflammation while glutamine, aloe, DGL, zinc carnosine, and Vitamin D can all help heal damage.

Sealing the deal by improving thyroid function.

Mainstream doctors only check levels of TSH and possibly T4 but that is just not enough to make an accurate thyroid diagnosis.  At a minimum levels of TSH, Free and total T3, Free and total T4, Reverse T3, and antibodies to thyroid tissue TPO and TBG should be checked. Antibody levels are almost always omitted by routine testing yet necessary to understand if there is an autoimmune process going on in the thyroid.  

Additionally I use a test called the TRH stimulation test which I find to be the most accurate and best way to diagnose thyroid function. There are instances where a more comprehensive blood panel may not reveal low thyroid function. The TRH however will catch even the difficult to diagnose cases.

When patients require thyroid treatment, I work with a compounding pharmacy to mix proportions of both T4 and T3 for the needs of each individual person. The hormone used is pure without any fillers or dyes that patients often react to.

Additionally, incorporating adaptogenic herbs to either soothe overworked adrenal glands or boost them after years of overuse can further protect the thyroid. Panax ginseng, rhodiola, ashwagandha, cordyceps, and IV’s of high dose Vitamin C, vitamins, and minerals all help reboot and find balance.  

Recommended Supplements

I manufacture a line of supplements that incorporate a custom blend of ingredients based on  my book The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss. I’ve also included here below my list of recommended supplements by brands I trust that can be found online and in stores.

Betaine HCL: Designs for Health Betaine HCL

Digestive Enzymes: Designs for Health Digestzymes

Probiotic: Probiotic 50B by Pure Encapsulations

Curcumin: Integrative Therapeutics Theracurmin HP

Glutamine & Aloe: GI-Revive by Designs for Health

About Raphael Kellman, M.D.

Dr. Kellman is a pioneer in functional medicine with a holistic and visionary approach to healing. In 17 years of practice, he has treated more than 40,000 patients worldwide helping them regain their health by gaining a deeper understanding of what it means to “heal”. He gets to the root causes of the disease by addressing the biochemistry, metabolism, hormones, genetics, environment, emotions, and life circumstances of his patients. Dr. Kellman is a graduate of Albert Einstein College of Medicine in New York and completed his postgraduate training in internal medicine at Beth Israel Hospital, Lenox Hill Hospital and St. John’s Hospital. The Kellman Center for Integrative & Functional Medicine is located in New York City.


1. Franceschi F, Satta MA, Mentella MC, Penland R, Candelli M, Grillo RL, Leo D, Fini L, Nista EC, Cazzato IA, et al. Helicobacter pylori infection in patients with Hashimoto’s thyroiditis. Helicobacter. 2004;9:369.

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About Dana Trentini

Dana Trentini M.A., Ed.M., founded Hypothyroid Mom October 2012 in memory of the unborn baby she lost to hypothyroidism. This is for informational purposes only and should not be considered a substitute for consulting your physician regarding medical advice pertaining to your health. Hypothyroid Mom includes affiliate links including the Amazon Services LLC Associates Program.


  1. Wow. Some of the research that supports the content of this article has only recently been published. To have written this in 2015 is very impressive. But I can top it. I got blood poisoning in Czecholslovakiia in 1974 when I was 11. I was given strong anti-biotics and my uncle Lubos forced me to drink Kefir. My uncle Lubos was a middle-aged aluminium smelter. How did an aluminium smelter in Communist Czechoslovakia know about probiotics and antibiotics? It still blows my mind when I think about it.

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