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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. What is your opinion on fecal transplant for patients with autoimmune problems including luck of beneficial gut flora and diversity?

    • It’s certainly possible that they would help, given how much of the immune system resides in the gut, but we have little research to say one way or the other at this point.

  2. I have hashimotos and DAO snp. My naturopath has suggested i refrain from any fermented foods. She feels the high histamine levels may be harming my gut. However without them i am concerned about missing the benefits.

    • You can get tested objectively for histamine intolerance. Dunwoody labs offers a test for DAO and histamine levels, and there are other markers for mast cell activation disorder that can tell you if you have this problem.

  3. Chris or anyone
    Do you know if LPS is produced by certain bacteria more than others? Can a person find out if their gut flora has a predominance of the type of bacteria which produce LPS? If yes – what test would show that? Thanks for a great article – concise and full of practical info.

    • It is produced primarily by gram-negative bacteria. This is the category of bacteria that most enteral pathogens fall into, so we might say that LPS is more typically produced by “bad bacteria” as a rule.

  4. Thank you so much for this information. I have appointment with a Dr on may17 and will share this with her if she doesnt already know.. You are certainly one of the best with all your information and so happy i have been following you for awhile about the conversion of t4 to t3. Just such a relief that you are getting to the bottom of this as i have been suffering for 35 years without ANYONE looking into this problem with any depth.. WONDERFUL you are.

  5. Chris, what is your probiotic of choice if a patient doesn’t tolerate fermented foods well? Vital 10?

  6. Hi Chris,

    I think I have a somewhat similar question to Angela above. It seems in most protocols, the answer to healing is first healing the gut through diet, supplementation and stress management. For me, the foods that are traditionally meant to heal, like bone broth, fermented foods and fermentable fibers are all things that actually exacerbate my symptoms that stem from SIBO, high levels of histamine and leaky gut. What is the best way to heal the gut when it seems the only option is probiotics and a diet that removes almost all foods? And taking into account that the person is leading a very low stress lifestyle? All things seem to circle back to “healing diets” but I find myself feeling very confused and lost as these diets seem to go against the diets that are prescribed (like Low FODMAPS, low histamine, etc) for most people who suffer from the symptoms the gut healing diets, including fermentable foods and bone broths, are meant to help.

    Thank you!

    • Exactly melanie!!! this is so frijkin hard! So typical with long standing candida sibo parasites hypo ad fatigue etc that mast cell issues starts and then its nothing left to eat ( all biogenic amines, fodmaps etc is out so how does one heai?? Pktease chris if you have any stggestion how to proceed( not all people can afford consulting you and tried to find another func med prac to no avail). Help us help ourselves chris!!

    • Antimicrobials to address the SIBO. In many if not most cases, SIBO cannot be treated with diet alone, in part for the reasons that you mentioned.

    • Melanie (and Marie),

      I empathize with the dilemma and I wanted to share a few things that definitely made a positive difference for me. With being grain, dairy, egg, nut and soy free my diet is very restricted as well. I’ve found that probiotics, fodmaps, and histamine were definitely issues for me so I researched a few things that were great.
      First I needed to eat more protein and fat. Marks Daily Apple is a great source for macronutient info on a paleo diet. Getting more than enough is essential as your body is healing and I found that the amounts made such a big difference.
      Two things helped me with SIBO and histamine issues. Histamine intolerance can come from the liver being backed up with histamine (thanks to the bacteria from SIBO) so I supplemented some sulphur. Sulphur is essential to opening liver detox pathways and I could feel a difference. Also, I wanted a prebiotic that didn’t exacerbate symptoms, so I tried resistant starch. It feeds the bacteria but also has a sweeping effect on the small intestine. Potato starch and plantains are good sources of resistant starch.
      Those things improved my symptoms greatly and histamine and fodmaps are not usually an issue now.

      • Hi Morgan,

        Thank you for sharing your journey and the things that have helped you. I will definitely look into them.

  7. I started having thyroid problems at the same time I was having problems with high blood pressure. I believe my hypothyroidism stemmed from staying away from salt and thus no iodine intake which is neccessary for a healthy thyroid. That was over 10 years ago. I had bad intentional problems a few months back with bleeding hemmoroids. 90% was cleared after I stopped eating whole wheat bread and oatmeal and used a hemmoroids suppository. Much improvement in my intestinal tract. Wondering now if I had a wheat allergy.

  8. Where can you get tested for SIBO like candida? I’ve been thinking I have it for months and trying to get rid of it with much stress but then without a doctor’s confirmation maybe I’m aiming in the dark. Thanks.

    • Some gastroenterologists test for SIBO, but you’re better off finding a functional medicine practitioner that understands the entire spectrum of functional gut pathologies.

      • Chris – Weren’t you planning to write a book on gut health?
        I’d be really interested in that.
        Also – what do you think about the brain to gut connection via the vagus nerve. If the vagus nerve is malfunctioning then that could be an underlying cause for SIBO. (vagus nerve is responsible for enzymes, stomach acid being produced and esp. the nerve activation that initiates intestinal motility and the valve action so needed to keep contents moving through and not backing up into the small intestine).

  9. I would never have made this connection in a million years but my sibo of nearly ten years with low thyroid was caused by an infection dominating from a root canal treatment in a back molar in my mouth. Everything resolved itself following removal of the tooth and a course of antibiotics. I became normal again very quickly and feel like I’ve got my life back. My doctor is still nonplussed but I’m delighted. Sometimes the answer is not what we expect.

  10. Another connection is between Hashimoto’s and celiac. I never knew there was a linkage until after I was finally diagnosed with celiac. All the factors you discussed are important, but i think the first step is to rule out celiac when thyroid function is poor.

  11. While the article abstract talks about hyperthyroid condition only, the article itself is about both.

    From the disucssion:
    ‘The results revealed that Enterococcus increased and Lactobacillus and Bifidobacterium decreased remarkably in the hypothyroid group. The Enterobacteriaceae and Clostridium increased in the hyperthyroid group, but there was no statistic significance.’ At another point in the article, they refer to the same change as ‘significant’.

    I am affraid some editting is in order – and the Publisher is going to have to do sth about the publication itself. When reading I get the impression that more mix-ups may have occured, possibly due to translation issues.

  12. Hello Chris,

    I feel that most of the articles on thyroid problems in relation to food/diet and gut seem to refer to Hypothyroidism/Hashimoto’s. I am suffering from Graves disease and multi nodular goiter and after a year of anti-thyroid medication, going gluten and dairy free and a gut-healing supplements, my TSH is unfortunately approaching 0 again. I have always had a healthy lifestyle and diet and have no idea what else I can do now to get back my health in a natural way. I would love it if you could devote some of your great research skills to shedding some light on the root causes and natural solutions for people with Graves disease and multi-nodular goiter. Also, I read that both high and low iodine can be a cause, which I find confusing.

  13. You have many reference numbers in the script but no references given at the ene of the article to follow up.

    • Each reference number in the article is a hyperlink that will open the reference in your browser.

  14. I have no doubt that the stress of losing my husband suddenly caused the shock which upset my adrenal glands. I already had a low thyroid level – but unable to take prescribed medication I managed very well with Lugols iodine up to this point. Within a week of my husbands demise I was vomiting at night, which progressed to daytime projectile vomiting. After hospital admissions due to sheer starvation with the pain ( waste of time) where they pumped me up with steroids and did quite a bit of damage elsewhere ( circulation) I later discovered I had SIBO which is not recognised here yet by doctors. I have since been treating myself for Sibo with digestives and bitters,and have it under control on a Paleo diet, still have a low thyroid which returns reasonable thyroid levels for blood readings with Lugols, Chlorella and spirulina.
    I now have developed painful Rheumatoid arthritis all connected with the above.I also take Sauerkraut, probiotics daily.
    I can cope with it all but how can I get some energy back? I am exhausted and want to move back to my home country( UK) where I can get some help with this lot.

  15. Chris,
    It makes sense that we need fermentable fiber for the reasons you list. However if one has leaky gut or gut lining damage then LPS will leak into the blood stream. Is it a matter of first healing the gut lining then adding the fermentable fiber?

    My understanding (from GAPS) is that to heal the gut lining one needs to omit starches from the diet for a time. I know you explored GAPS. Do you disagree with the GAPS protocol and others that say you need to avoid grains and root starches like the ones you listed in order to heal the gut lining?

    • I agree that if you have leaky gut then fibre is really a no go zone initially. No vegetables at all.
      My own adapted Gaps diet.
      Cooked fatty minced beef.
      Bone stock
      Over cooked white rice.
      Lots of butter.
      And that’s all I really lived on for several months. breakfast lunch dinner.
      Help heal my gut tremendously.

      • Tim,
        Sounds like you found the right approach using GAPS for you.
        my guess is that the key is using GAPS or other no starch protocols TEMPORARILY. Then follow with gradually adding the right kind of starches (prebiotic), in small amounts to feed good bacteria. I just wanted to hear from Chris K. on this since I know he has advocated GAPS in the past. But this article doesn’t acknowledge the benefit of doing a phase without starches.

        • For some it may be necessary to reduce or eliminate starches for a period of time. The goal, however, is always to address the underlying gut pathology and eventually reintroduce fermentable fiber to promote the long-term health and diversity of the gut microbiome.

      • This is fine for the short term, but over the long term it will starve the beneficial bacteria and reduce microbial diversity, which numerous studies indicate puts us at higher risk of disease and early death. We always have to be careful with solving one problem but causing others down the line.

  16. Thank you, Chris, for the extremely informative article. I was diagnosed with Hashimotos 21 years ago, after I’d been taking antibiotics continuously for about 10 years. Since I started eating cleaner, mostly raw, and gluten free three years ago, the prescribes dosage of my synthetic thyroid supplement has been decreased by 30%. Using the information you’ve provided regarding gut microbiome health, I hope to accelerate my healing process. Healing is something that some of us have to work at, and it is not so easy. But our bodies are so amazing, I believe that anyone can heal if they provide it what it needs.

  17. Is this why when I was 14 years old, my period started for 1 day and then stopped? The endocrinologist gave me a thyroid hormone pill for one day and it started up. I have had thyroid benign tumor, goiter.
    I also suffered from hypochondria, costocondritis, anxiety, depression, headaches.
    I also was never breast fed and prematurely born 1 month. I was given antibiotics in high school for acne back in the 70’s. I suffer with chronic dysbiosis and systemic tissue fungal overgrowth. It’s been a nightmare for my whole life because western medicine had no clue about the gut micro biome. My time here on earth is short.
    My mother has no clue how important it was to breast feed and to not drink 2 martini’s a night and smoke while her baby was in her womb. I also suffer with genetic defects.
    I take one day at a time and pray for God’s kingdom to come.

    • I think i have this too. Finally got my Western Medicine doctor to agree iaybe the cause of declining health at 45.
      Antibiotics kill and Western medicine is getting a way with damaging many lives, including children!
      Enough of the cover up!

    • @Ann.
      You are not alone. I struggle with celiac/hashimoto’s everyday also. I also was not breast-fed….had multiple mercury fillings..and was raised on white bread and processed meats and oils. I have been on Paleo/GAPS…you name it diet only to be defeated. Had mercury fillings removed several years ago and continue to have failing health. I have purchased all the Leaky Gut books and Autoimmune books out there..purchased tons of supplements and still….SICK. So yes…we wait for God’s kingdom.

      • Having mercury fillings removed does not remove the mercury stored in the body. Homeopathic mercury chelation plus supplementing with the minerals (such as magnesium and zinc) that are blocked by mercury will greatly enhance your well-being. Having an Oligoscan will help to determine what you need.

    • Anne, how did you find out you had chronic dysbiosis and systemic tissue fungal overgrowth? Did you have a specific test done? Just curious. My husband suffers from gastro issues and no one can tell us what’s wrong. Has had every test under sun. Thanks

  18. In addition to low thyroid, I’m also type2diabetic, or pre-diabetic some days, controlling that through diet. So what I would like to do for my bloating, is to consume ferment able fiber, but the sources that you mention, Chris, will also increase my blood glucose. Any other suggestions?

  19. I think the SIBO causes the thyroid problem. I know that SIBO causes fatty acid malabsorption even though, according to the endoscopy, my villi are fine. I just wish I knew how to compensate for the maldigestion of fat-soluble vitamins. I don’t think you can fix your stomach until you are getting the nutrition that the bacteria are eating, because I have tried.

    • I have found the same thing to be a problem for me. Serum testing shows micronutrient deficiencies (magnesium, iron, etc.). I don’t know how to increase my levels because oral supplementation seems to be a losing battle because I have SIBO (confirmed via breath test). Would love advice on how to get ahead of the microbes when it comes to absorption. I eat healthy (expensive!) good and take high quality (expensive!) vitamins. But I don’t know how much is making it through to my cells.

    • I think my absorbtion is bad in general. I’ve decided to use a couple of packs I bought off amazon to clear candida (google it, don’t even like explaining it!). I’m also about to add probiotics to my diet for a month. Swansons do a really high density one. Amazon too. And to reduce stress while in an effort to counter all aspects I’m adding ashwaganda. 6 weeks of good low low sugar diet plus this and I’m hoping to feel much better v