The Thyroid Gut Connection

Thyroid conditions, such as Hashimoto’s thyroiditis or hypothyroidism, are typically associated with symptoms such as infertility, hormonal imbalances, weight gain, fatigue, or anxiety.

However, what’s lesser known is that digestive/gut health issues, such as indigestion, acid reflux, bloating, constipation, IBS, etc. can be telltale signs of a thyroid issue.

And since thyroid and gut health conditions are often overlooked or misdiagnosed, it’s important to understand the thyroid-gut connection so you can advocate for yourself effectively.

The link between thyroid function and gut health

I often feel like the thyroid is one of our body’s most underappreciated work horses.

Not to downplay the importance of more “celebrity” organs like the heart, lungs, etc. but seriously, your thyroid is responsible for so many bodily functions it’s kind of insane.

For example, thyroid hormones play a key role in things like our ability to conceive, our sleep patterns, our mental health, our energy levels, and how well we digest, assimilate, and absorb our food and nutrients.

That’s because thyroid hormones like thyroxine (T4) and triiodothyronine (T3) define basal metabolism (the amount of energy expended to complete a biological task/function) throughout the entire body, particularly in the intestine and internal organs.1

It’s well documented that thyroid and digestive issues often coexist2, and the liver is the most affected organ in both hypothyroidism and hyperthyroidism.3

Gastrointestinal symptoms of thyroid dysfunction are numerous, and include trouble swallowing, heartburn, indigestion, reduced acid production, nausea or vomiting, gallbladder complaints, abdominal discomfort, gas, bloating, diarrhea, constipation, and general digestive complaints including Irritable Bowel Syndrome (IBS).4

It’s also been well-documented that an imbalance in gut bacteria/gut infections can affect the thyroid; so it’s a two-way street.

Intrigued? Let’s dive in!

The thyroid-gut-autoimmunity connection

A healthy gut microbiome impacts the immune system, and also has an important influence on thyroid function, specifically on autoimmune thyroid diseases like Hashimoto’s thyroiditis and Graves.5

Hashimoto’s and Graves often coexist with specific digestive diseases, including Celiac Disease and Non-celiac wheat sensitivity (NCWS).6,7 In fact, research shows that people with autoimmune thyroid disease are 4 to 5 times as likely to develop Celiac Disease as the general population.8

Autoimmune issues, in general, have a strong association with gut health. This can be explained (at least in part) by compromised intestinal barrier function (aka: intestinal hyperpermeability or “leaky gut”) which allows antigens to pass more easily and trigger autoimmune disease in genetically susceptible individuals.9,10

As our understanding of the gut microbiome grows, we are seeing evidence that the collection of organisms living inside us plays a role in hypothyroidism and autoimmune thyroid disease.

For example, research has shown that shifts in gut microbiota, including dysbiosis, can affect your overall thyroid health and even cause and exacerbate autoimmune thyroid disorders, including Hashimoto’s.11,12

A 2007 study found among people with a history of autoimmune hypothyroidism, 54 percent had a positive breath test for SIBO (small intestinal bacterial overgrowth) compared to 5 percent of controls.13.

Since thyroid hormones are also essential to gut motility14 (how your food moves through your intestines) it serves to reason that motility issues could create the “perfect storm” for unhealthy bacteria to flourish in the small or large intestine. In other words: it’s a vicious cycle!

It’s also important to note that you can have a gut health/thyroid issue with little or no gastrointestinal symptoms.

For example, thousands of people are diagnosed with Celiac Disease every year after showing up at the doctor’s office for an entirely different (non digestive) issue.

Same goes if you have autoimmune thyroid disease like Hashimoto’s. You may think your gut health is fine because your doctor didn’t ask you about it… However, given the simultaneous prevalence of gut and thyroid issues it’s a good idea to find a functional medicine doctor to have your gut health checked.

How the gut influences the thyroid

The composition of our gut bacteria, or microbiome, affects our bodies ability to assimilate and absorb key micronutrients such as iodine, selenium, zinc, iron, B-vitamins, vitamin A, and tyrosine—all of which are essential to healthy thyroid function. These micronutrients are often deficient in those with autoimmune thyroid disease.15

Although not fully understood, gut microbiota also influence the conversion of T4 to T3—T3 being the active form of thyroid hormone. Iodothyronine deiodinase enzymes play a central role in the conversion of T4 to its active form T3. It is hypothesized that the intestines and gut microbiota influence the activity of these enzymes.16

At least in part this is attributed to the influence of gut microbiota on the availability of micronutrients like selenium and zinc which are needed for converting T4 to T3.17,18

But likely it goes further than that…as deiodinase activity has been found in the intestinal wall, and at least one animal study shows the ability of gut bacteria to bind thyroid hormones [1,25].19

Here’s where this gets really interesting: the success of this process is also largely dependent on the production of primary bile acids in your gallbladder. These primary bile acids are secreted from the gallbladder into your small intestine following the consumption of fats, where gut bacteria metabolize them into what’s known as “secondary bile acids” which increase activity of the deiodinase enzymes.20 What’s more, these bile acids are dependent upon the aforementioned mineral selenium, which is often depleted in patients with gut and thyroid health issues.21 And hypothyroidism has also been shown to impede bile flow from the gallbladder which further affects T4/T3 conversion.22 This bile is also naturally antimicrobial, which may further explain the connection between thyroid disease and specific bacterial gut infections, like SIBO.

Can you say vicious cycle?

This is by no means an exhaustive review of all the ways the thyroid impacts the gut (many of which I’m sure are yet to be discovered), but it further validates the connection and interconnection between the two systems.

How the thyroid influences the gut/digestive system

You’re in deep now, so let’s continue by exploring how the thyroid affects the gut and entire gastrointestinal/digestive system.

We’ll start with the most familiar players in your digestive symphony: your mouth and stomach.

As you probably remember from grade school biology, digestion begins in your mouth with the production of enzyme-rich saliva which initiates the breakdown of food, specifically starches. So, it’s really important to have enough saliva production to get this process started off right.

However, research has shown that a significant amount of people with autoimmune thyroid disease, such as Hashimoto’s, lack adequate amounts of saliva and experience “dry mouth”. 23 This is due in part to the over-production of pro-inflammatory cytokines which hinder normal production of saliva.

Your thyroid also plays a super important role in production of stomach acid which can result in symptoms like GERD, nutrient deficiencies, and other digestive ailments like SIBO (small intestinal bacterial overgrowth) and SIFO (small intestinal fungal overgrowth).

Research has also shown that hypothyroidism causes gastrointestinal dysfunction by significantly reducing gatroesophageal motility (aka: movement), and thus, it is recommended thyroid function be checked in patients with indigestion.24

Studies also show the link between atrophic gastritis and autoimmune thyroid disease.25

This is why many people with low thyroid function benefit from supplementation with Betaine Hcl. (If you want to learn more about this I suggest you read this article from my friend and colleague Izabella Wentz PharmD, aka The Thyroid Pharmacist.)

But there’s more!

There are other organs that play a crucial role in the proper assimilation, break down, and absorption of macro and micronutrients which are also impacted by thyroid health.

For example, your liver produces enzymes and bile essential to digestion and assimilation of proteins, sugars, and fats. It also works hard to metabolize toxins (like pesticides or heavy metals), alcohol, and control the amount of glucose released into your bloodstream.

In other words: if your liver isn’t functioning properly your digestion will be off.

However, your liver cannot function optimally without (you guessed it!) a healthy thyroid, and research has shown the liver is the organ most affected by hyper- and hypothyroidism.26

So, an unhealthy thyroid makes for an unhealthy liver which affects the gallbladder and hampers optimal digestion, nutrient absorption, and T4/T3 conversion (as discussed in the previous section)…not a pretty picture.

Further, your pancreas and thyroid share a connection, with the thyroid showing influence over pancreatic enzyme production and overall functional integrity.27

Finally, there are the numerous connections to intestinal function, such as altered motility, which we’ve discussed previously.28. To bring it full circle, altered motility is a setup for constipation, but also bacterial overgrowth, which is one reason for the strong association between hypothyroidism and SIBO.29

Does any of this sound familiar? Here’s what gut/thyroid tests to ask for

If you’re having lights go on all over the place about your unresolved digestive and/or thyroid symptoms, here are some of the tests I recommend to my patients:

  • A full thyroid panel, which includes TSH, free T4, free T3, reverse T3, as well as Thyroglobulin (TG) and Thyroid Peroxidase (TPO) antibodies. To learn more about why I run all these tests, and not just TSH, check out: A Functional Medicine Doctor’s Approach to Hashimoto’s Thyroiditis and Hypothyroidism.
  • Complete Blood Count (CBC) and Iron Panel to check for anemia and iron levels
  • Nutrient testing for zinc, selenium, Vitamin D, Vitamin A, and some of the B vitamins (homocysteine can be a helpful marker for B vitamins as well)
  • Iodine testing can be helpful as well, though cumbersome. The best test is a 24 hour urine iodine, though I find checking a spot serum iodine to be clinically useful.
  • Organic Acids Test (aka: OAT), a urine test which screens for a variety of factors including nutrient levels and fungal overgrowth or dysbiosis.
  • GI Map, a stool test that screens for a number of intestinal pathogens, as well as other markers for intestinal health like enzyme function and fat malabsorption.
  • SIBO breath test, which measures hydrogen or methane gas produced by overgrowth of bacteria in the small intestines.

Healing solutions for gut/thyroid imbalances

Once you know what you’re dealing with (SIBO, candida, Hashimoto’s, hypothyroidism, etc.), it’s time to start implementing a healing strategy to address the root cause.

In my practice, this usually includes the following:

A custom nutritional plan

This involves eliminating trigger foods which cause unwanted symptoms and/or feed pathogens. This differs person to person, but I consistently recommend eliminating gluten for patients with autoimmune disease based on research which shows the connection between gluten, zonulin, and autoimmunity.30

What else should you stay away from/limit? Anyone with a gut health issues generally benefits from cutting back or eliminating refined/processed carbs, refined sugar, and artificial sweeteners. Food sources of heavy metals (such as large fish) as well as pesticides should also be avoided, when possible.

We also work on increasing your intake of nutrient-dense foods including foods high in selenium, zinc, iron, B vitamins and vitamin A, and foods rich in healthy fats like olive oil, nuts, avocados, and omega-3s.

The right medications

While medication may not be necessary for every circumstance, I am an advocate of using safe, properly-dose medication for specific thyroid and gut health conditions. A few of the medications I commonly prescribe include thyroid hormones like Tirosint or Armour, and Low Dose Naltrexone (LDN). But, as always, this is an individualized discussion to have with your provider based on risks and benefits.

A personalized supplement regime

Since so many people with gut/thyroid issues have nutrient deficiencies, I typically recommend supplementing with things like a high-quality multivitamin with vitamin A, methylated B-vitamins, iron, selenium, vitamin D, and zinc in addition to dietary changes.

For many patients, I also recommend probiotics, typically MegaSporeBiotic either immediately or at some point during the healing process depending on the diagnosis.

Adaptogenic herbs, like Ashwagandha, can also be beneficial to support a healthy stress response and calm the nervous system.

In my practice, personalize these recommendations based on testing and your unique needs and vulnerabilities.

Lifestyle changes

I always counsel my patients on how to adopt a low-tox lifestyle, which means drinking clean filtered water, breathing clean air (especially inside the home/office!), and eating clean food.

Some examples of this include: removing heavy metals such as amalgams (but please, only do this with a trained IAMOT dentist…otherwise let sleeping dogs lie!), reducing stress, daily movement and restorative exercise, getting enough sleep (8-9 hours a night), spending time in nature, getting off hormonal birth control if possible, and addressing emotional trauma with a trained therapist.

For more tips on creating a truly low-tox lifestyle, download my free ebook 12 Ways To Detox Your Home.

Ready to do something about your chronic digestive issues and/or thyroid health?

I’m currently accepting a limited number of new patients for functional medicine consults…and thyroid health, autoimmunity, and gut health are three of my specialities.

Click here to learn more about becoming a patient, and I look forward to hearing from you!



About Dr. Maren

Christine Maren D.O., IFMCP is a board-certified physician and the founder of a virtual functional medicine practice in Colorado, Michigan, and Texas.  She is best know for her work in thyroid, gut and reproductive/ preconception health. Dr. Maren is board-certified by the American Board of Family Medicine and is an Institute for Functional Medicine Certified Practitioner (IFMCP)

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