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Your Gut Microbes and Your Thyroid: What’s the Connection?


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While there are many factors that influence thyroid function, recent research suggests that gut health may be a key player. The trillions of microbes that reside in your gut have a profound influence on the production of hormones in the body—including thyroid hormones. Read on to find out if a disrupted gut microbiome might be contributing to your thyroid problem, and learn how healing your gut could improve your thyroid function.

thyroid gut connection
Having issues with your thyroid? The answer might be in your gut. iStock.com/fotostorm

A central principle of functional medicine is addressing the underlying cause of a disease, as opposed to just treating symptoms. In a previous article on the blog, I discussed the connection between overall gut health and the thyroid. In this article, we’ll focus on the microbes themselves and the many ways in which they are connected to thyroid function.

The Importance of Microbes and Their Metabolites in Endocrine Health

In recent years, the microbiota has been implicated in numerous chronic diseases, from obesity to inflammatory bowel disease to multiple sclerosis (1). It really should be no surprise that it also has a profound impact on endocrine organs like the thyroid. Disruption of the intestinal flora and subsequent impaired thyroid function was first hypothesized back in the early 1900s, long before the terms “microbiota” and “microbiome” were even coined (2).  

Today, microbial sequencing of human fecal samples allows us to measure compositional differences in the microbiota. A 2014 study found that individuals with hyperthyroidism had significantly lower numbers of Bifidobacteria and Lactobacilli and significant higher levels of Enterococcus species compared to healthy controls (3). No equivalent study has yet been done in individuals with hypothyroidism, but given that 90 percent of hypothyroid cases are autoimmune in nature (4) and the fact that an altered microbiota has been implicated in countless other autoimmune diseases, it’s quite likely that dysbiosis plays a significant role (5).

Will healing your gut improve your thyroid function?

Microbes recognize a number of different host endocrine molecules, including adrenaline, noradrenaline, sex hormones, and thyroid hormones, and can even change aspects of their metabolism and virulence in response to these signals (6). Moreover, germ-free rats, which are raised in sterile conditions and lack gut bacteria altogether, have smaller thyroid glands than conventionally raised rats, suggesting a crucial role for these microbes in thyroid health (7).

Gut Bacteria Influence Nutrient Availability

The epithelial cells that form the lining of the gut have fingerlike projections called villi, which increase the surface area for transporting nutrients into the body. When the gut is inflamed, as is often the case with microbial dysbiosis, these villi can become truncated, resulting in impaired nutrient absorption. This includes nutrients like iodine and selenium, which are vital for thyroid health.

While the microbiota provides many benefits to the host, it also competes with the host for nutrients. The nutrients that are essential for our cells to function properly are also important nutrients for our microbes!

The composition of the microbiota may therefore influence a person’s requirement for various nutrients. In fact, a 2009 study in mice suggested that the microbiota competes with the host for selenium when selenium is scarce, impairing synthesis of selenoproteins, which are necessary for proper thyroid function (8). In another study, rats fed kanamycin, a broad-spectrum antibiotic, had significantly lower iodine uptake by the thyroid (7).

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Gut Bacteria and LPS

Lipopolysaccharide, or LPS, is a component of bacterial cell walls. When intestinal permeability is increased, often as a result of gut dysbiosis, LPS can “leak” into the bloodstream. This can wreak havoc on the thyroid in a number of ways.

Thyroid-stimulating hormone (TSH) induces the thyroid to produce T4. T4 is the inactive form of thyroid hormone and must first be converted to T3, the active form.  Our bodies produce an enzyme called iodothyronine deiodinase that is responsible for making this conversion. LPS has been shown to inhibit this enzyme, decreasing the amount of active T3 in circulation (9).

Not only do you need active thyroid hormone, but you also need receptors for thyroid hormone on cells throughout the body. Even someone whose thyroid hormone panel looks perfect could suffer from symptoms of hypothyroidism if their body does not produce enough receptors to receive signals from the thyroid. LPS has been shown to decrease expression of thyroid receptors, specifically in the liver (10).

LPS also induces expression of the sodium-iodine symporter (NIS) in thyroid cells, increasing iodine uptake in the thyroid (11). Since iodine is important for thyroid health, this might sound like a good thing, but excess iodine (especially with concurrent selenium deficiency) has been found to contribute to the development of Hashimoto’s, the autoimmune form of hypothyroidism (12).

Gut Bacteria Influence Conversion of T4 to T3

Remember in the last section how we said that inactive T4 must be converted to active T3? Well, about 20 percent of this conversion takes place in the GI tract! Commensal gut microbes can convert inactive T4 into T3 sulfate, which can then be recovered as active T3 by an enzyme called intestinal sulfatase (13).

Bile acids present another interesting connection between gut bacteria and thyroid function. Primary bile acids are produced in the gallbladder and secreted into the small intestine following the consumption of fats. Metabolism of primary bile acids by the gut bacteria results in the formation of secondary bile acids. These secondary bile acids increase activity of iodothyronine deiodinase (the main enzyme that converts T4 into T3) (14).

We’ll see one more way that gut bacterial metabolites influence thyroid health later when we talk about prebiotics.

SIBO and the Thyroid

Thyroid function is also closely related to small intestinal bacterial overgrowth (SIBO). In a healthy individual, the majority of microbes are concentrated in the large intestine. In SIBO, certain bacteria and archaea are able to colonize the small intestine and proliferate, causing bloating, gas, and distention, among other unpleasant symptoms.  

The connection between SIBO and the thyroid is underappreciated. A 2007 study found that among people with a history of autoimmune hypothyroidism, 54 percent had a positive breath test for SIBO compared to 5 percent of controls (15). It is currently unknown whether the relationship is causal.

Since thyroid hormones help stimulate gut motility, it is also possible that low motility and constipation provide an environment in the small intestine that is conducive to bacterial overgrowth.

This may be one of many examples of bidirectional interaction between the host and its resident microbes.

Conclusion: Heal Your Gut to Improve Thyroid Function

So how can we apply this information? Here are four ways that you can improve your thyroid function:

  1. Eat plenty of fermentable fiber
    Bacterial metabolites are potent endocrine modulators. When you consume fermentable fibers like cassava, sweet potato, or plantains (prebiotics), your gut bacteria ferment these fibers and produce short-chain fatty acids (SCFAs). SCFAs have been shown to inhibit enzymes closely involved in epigenetic regulation. In other words, they help determine whether a gene is expressed or not. Among many other things, SCFA-mediated inhibition of these enzymes increases expression of thyroid receptors (16).
  2. Take probiotics or eat fermented foods
    Despite the long-hypothesized link between gut microbes and thyroid function, there are few controlled studies in humans that have tried manipulating the gut microbiota to improve thyroid health. However, supplementation in broiler chickens with lactic acid bacteria has been shown to increase blood plasma thyroid hormones (17), and Lactobacillus reuteri supplementation specifically improved thyroid function in mice (18). Lactic acid bacteria are commonly found in fermented vegetables such as sauerkraut and kimchi and fermented dairy products like yogurt and kefir.
  3. Get tested/treated for SIBO or intestinal pathogens
    While the jury is still out on whether thyroid problems cause SIBO or SIBO causes thyroid problems, it certainly doesn’t hurt to get tested, especially if you are experiencing bloating, abdominal discomfort, or other symptoms characteristic of an overgrowth or infection.
  4. Take other steps to heal your gut
    Remove inflammatory foods, manage stress, and eat a nutrient-dense diet that includes plenty of gut-healing foods like bone broth. For some people, healing the gut may be sufficient to ameliorate thyroid symptoms.
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Join the conversation

  1. I have Hashimoto’s and also am being treated for low pancreatic enzymes. I recently started a holistic three product program that focuses on balancing the Gut-Brain Axis. Within the first month of the program I was able to lower my dosage of Synthroid and eliminate an expensive digestive enzyme(Zenpep).

  2. I’ve been hypo for 15years, dx’d with Hashi’s as well. Now I have large, possibly cancerous (biopsy showed FLUS ) in 2 nodules and something else in the 3rd, fast growing nodule. I am having my whole thyroid removed this Friday. What I’m having a hard time finding are recommendations for people who no longer have a thyroid.

    I get that we want to heal the thyroid, but what about those of us who for whatever reason don’t have one. Are there specific recommendations you can make?

    • Jodey, I’m sure Chris will give you excellent advice but maybe also look on Amy Myers’ website as she has had her thyroid removed and seems to be an expert on the thyroid.

  3. Hi Chris and all, Huge fan! About me: 31yo M, 5’9 135lb (from 150lb). I was just diagnosed with hypothyroid by my ND. Low T3 (.6!), high LDL, low alkaline phosphatase, low HCT. What my ND told me is basically border-line anemic (but my iron levels are great) and need to take Cytomel. This is after a 10year battle trying to figure out my IBS, with IBS-A and constipation. The thing is I’ve been losing weight, have enormous stools (lots of undigested food), but otherwise feel fine. Stool tests also reveal complete lack of ANY good bacteria. So I’m wondering if Cytomel to fix thyroid is enough, or if I need to supplement with selenium, iodine, etc. Unlike typical hypothyroidism, I don’t have weight gain (in fact weight loss) but have mild coldness and mild brain fog/tired. This all started with trying to regulate digestion so I wasn’t spending 1.5hr in bathroom daily, and now it’s progressed to thyroid! Thoughts?

    • I have similar symptoms from past one year. First it was hyperthyroidism with a few Kgs of weight loss,then it went hypo.no weight gain. Just bloating and gas.mild brain fog. Hemoglobin is just inside the border.not anemic. Sometimes feel diZiness.am finding relief in Ayurvedic medicine.

  4. I found Paleo Plus to work well for me as I live my life with Hashimoto thyroiditis. As per the Dutch Test my cortisol levels are very low all round with it highest at night. I have tried sooooo many things, Magnesium, DHEA, Pregnenolone, T3, T3 and T4 combinations, NDT like Nature Throid, T4 only as Levoxyl, I got the spasm after being on Tirosint. yet I find that my whole body shakes within a short time after taking my thyroid medication. The shaking at times are sooo bad that I can not write or even hold a cup properly. I also seem to get muscle spasms in both my left and right arms causing a jerk like movement. How can I stop the adrenaline surges and how can I ensure that I do not have an electrolyte imbalance. I eat gluten, dairy, grain free, have good fats, bone and meat broths, low carb and have sweet potatoes, udi’s bread and squash for carbs. use only coconut and olive oil.

    Thanks for any feedback

  5. Thank you Chris for this article. I’ve had low thyroid for quite a few years and none of the medical people I’ve seen here in the UK have ever been able to explain why I seem unable to convert T4 and have to take both T3 and T4. In fact at first they never believe that is the situation and I’ve had to go through extended periods of unwellness while I’ve been taken off T3 so they can try to prove their point! I’ve been gluten free for most of this year and while I’m not paleo because I don’t eat meat, I have been following other paleo advice and recently have felt I needed to reduce T3 a little which seems promising.

  6. Locally we have had a lot of problems with water and food contamination. (PFOA, Roundup, etc).
    Could this be a factor in the distruction of beneficial gut bacteria. Perhaps the constant exposure to contaminants IS the reason for the increase in inflammation.
    Yes, eating grains for instance can create inflammation on their own, but along with the natural poisons come a whole host of chemical poisons.
    I would think testing your water, and local environment (house, yard,etc.) should be done first, or at least along with all the things people mention here.

  7. As i know thyroid-stimulating hormone (TSH) produced by the pituitary will be decreased in hyperthyroidism. Thus, the diagnosis of hyperthyroidism is nearly always associated with a low (suppressed) TSH level. If the TSH levels are not low, then other tests must be run.

  8. I have Hashimoto’s and have been treated for SIBO nearly twice a year for the past 3 years as well as Yeast dysbiosis twice. I have IBS sx that I never had before and have been on a clean anti-inflammatory diet for the past 3 years. I had >40 food sensitivities from leaky gut and have improved in that area. Still dealing with the hormone imbalances and poor metabolism with many vitamin/mineral deficiencies. I have SIBO again now and am not able to tolerate the herbal treatment (biocidin). I’m suspecting Lyme but testing is inconclusive. I don’t tolerate detox diets very well.