Microbiome Health is the Foundation of Thyroid Health

gut pathogens and your thyroid health

Those microscopic, highly pathogenic, and darn clever organisms have the power to disrupt your thyroid health.

Written by Raphael Kellman, MD

The thyroid gland and the microbiome are intricately connected. The function of one affects the function of the other. As the thyroid plays many critical roles, the microbiome must be healthy to meet its demands. Good health is when the microbiome is diversified and abundant with bacteria. When the microbiome is dysfunctional, the thyroid will suffer. 

Thyroid Hormones & Healthy Gut Bacteria

The gut bacteria support thyroid function through several critical roles. The thyroid produces two main hormones – T3 and T4. T3 is the active form of thyroid hormone. Your body produces less T3 than T4 but converts the T4 to T3 when needed. It is the gut bacteria that converts about 20% of your stored T4 into T3. If you can’t convert enough T4 into the active form T3 you become hypothyroid. Your body needs iodine to make those hormones, and it is the gut bacteria that retrieves the iodine from food and delivers it to your thyroid. The gut also breaks down selenium from food into usable forms and sends that to your thyroid as well. Without these iodine and selenium deliveries, thyroid function is impaired. The gut also increases the amount of hormone that reaches the blood. 

Escherichia coli

Your Thyroid & Pathogenic Gut Bacteria

What happens to the thyroid gland when the bacteria are unhealthy? Pathogenic bacteria grab some of the nutrients that your thyroid needs, including iron and selenium. It becomes much harder for your thyroid gland to produce their crucial hormones. Pathogens produce a toxin called LPS that causes inflammation. One danger of inflammation is that it inhibits absorption of nutrients. To make matters worse, the remaining nutrients can’t be delivered to where they’re needed. 

Helicobacter pylori

What Sets the Stage for Bacteria to Become Pathogenic

A diet that contains processed foods, sugar, chemicals, too much fat and not enough plant-based food, overuse of anti-biotics, toxic exposure, chronic stress, even adverse childhood experiences – can all throw your gut into disarray. I work with patients on all of these issues, but none are more emotional – and critical – than working on Adverse Childhood Experiences (ACE’s). Age also alters the gut composition. Each of these on its own can cause tremendous problems, and as a combination it’s much worse. 

Leaky Gut & Your Thyroid

Leaky gut or a permeable gut wall can cause thyroid dysfunction. The lifestyle and environmental factors involved in creating pathogenic bacteria can also create leaky gut. This common microbiome dysfunction occurs when the intestinal lining – the barrier that separates the intestinal wall from the blood stream – is worn thin. Eventually it becomes so porous that it develops mesh-like holes. These breaks in the fabric of the intestine allow particles to leak through and enter the blood. Infection and inflammation are the first responses. The body sees these toxin fragments, food particles and pathogens as foreign invaders. The immune system, most of which resides in the gut, turns on itself, attacking its own tissue and creating autoimmune disease. Autoimmunity can manifest as many different diseases. The autoimmune disease of the thyroid is Hashimoto’s, and accounts for more than half of all hypothyroid cases.


A Better Approach to Thyroid Testing

The thyroid is involved in multiple diseases, so it’s critical that we maintain its health. The only adequate assessment, in my decades of experience, is the TRH Stimulation Test. It is the quintessential test – one that shows much more detailed information than standard thyroid tests. We are able to diagnose and treat so many people who have been previously told that their numbers were “normal” by using this one test. This one test has changed lives. 

About Raphael Kellman, MD

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 Wellness Center is located in New York City. He shares his groundbreaking program in the book The Microbiome Diet.


Hays MT. Thyroid hormone and the gut. Endocr Res. 1988;14(2-3):203–224.

Ihaq HM, Mohammad IS, Shahzad M, et al. Molecular Alteration Analysis of Human Gut Microbial Composition in Graves’ disease Patients. Int J Biol Sci. 2018;14(11):1558–1570. Published 2018 Sept.


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About Dana Trentini

Dana Trentini 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. Preach. I am a Graves disease patient, who suffered with interminable gut issues for years before being dx’ed, only to have a doc test for and identify h pylori in my stomach. After treating it, the gut issues did get better- but there was no effect on Graves. Something in me kept saying that there must be a link between the two, so I kept reading up. Come to find out… h pylori, an extremely well adapted bacterium to the human gut, exhibits molecular mimicry that renders it similar on a molecular level to… the thyroid. Idea being, the immune system would ignore the h pylori, believing it is ‘self’. And in the majority of the cases, that is what happens. However, for the lucky few (genetically predisposed? environmentally triggered? who knows), the immune system (of which +70% resides in the gut) does detect this bacteria as ‘non-self’, and mounts an attack vs. it. This is one extremely hard to kill bug, though. So the immune system is relentless in its attack. Given enough time without treatment, the h pylori molecular mimicry to the thyroid serves to confuse the immune system, which then starts attacking the thyroid as ‘non-self’. There are several studies regarding the link between AITD and h pylori. So completely agree, gut health, and its bacteria, are of paramount importance.

  2. Concerned about hair fall out? Have been tested & was told that I’m low in iron & nothing wrong with my thyroid? I do have type 2 diabetes 🤔

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