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

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

by Chris Kresser

Last updated on

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.

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).

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.

Now I’d like to hear from you. Did you know about the connection between the microbiota and the thyroid? Have you noticed any improvement in your thyroid symptoms by eating a gut-healing diet? Share your experience in the comments section!


Join the conversation

  1. 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.

  2. 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 weight gain. Just bloating and gas.mild brain fog. Hemoglobin is just inside the border.not anemic. Sometimes feel finding relief in Ayurvedic medicine.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Fantastic article on gut microbes and absorption. Coffee is a great one to avoid because it can block the absorption of much needed minerals from our daily diet

  9. I have issues with low thyroid, gut/GERD issues and low cortisol. The result of the adrenal issues is that I am extremely sensitive to any medication, most supplements or attempt to detox. Does your practice help people slowly gain more tolerance? I can’t fix anything with supplementation until I can improve my liver clearance. Thanks!

  10. Hi dr. Kresser,
    I’ve been dealing with Hypothyroidism for quite sometime. I know my ph is bad showing me to be very acidic, I have horrible gerd, my physician feeds me synthroid (which seems to help), I’ve been growing a gut without even trying, And I lose energy and strength while trying to work hard or just taking a high impact walk. One of the best things I’ve tried is wild flower honey that I purchase at local farmers markets. It helps with my gut and sinuses.
    I am very appreciative of this article on the thyroid to gut relationship and will put to practice what you advise ASAP.
    Thanks Doc.

    • Chris is not a “doc” he is a L.Ac. Just read your post, you can take a look at his other articles. Especially one where he refutes the acid/alkaline hypothesis

    • Honey is very acid forming. It will only increase the acidity in the body. The microorganisms in the honey are good for us though.

  11. I never really thought about the link between gut bacteria and thyroid. This article made me consider that with the impact gut microbes have on thyroid they also regulate the metabolism as well, completely fascinating…

  12. I read your article about hypothyroidism.
    I was diagnosed with rheumatoid arthritis a year ago. I am taking methotrexate orally, 12.5 mg 1 x week, in addition to lots of other supplements to try and calm the inflammation and balance the gut micro biome.
    I have just been diagnosed with hyperparathyroidism, with a high blood calcium level (10.9-11 mg/dl) and high PTH level (87 pg/ml).
    Your article only speaks about the thyroid and inflammation in the gut. But would my hyperparathyroidism be also caused by gut inflammation?
    I had a Sestamibi scan which did not show tumors, however I have heard they are not reliable. I am scheduled to have surgery to search for and take out likely tumors on the parathyroid glands. Thank you for any insight.

  13. Hi Chris
    My daughter had a complete parasitology test and has D. Fragilis, high E. Coil and zero lactobacillus and zero Bifidobacteria bacteria. She has taken Paromomycin for the parasitic infection. Will it be possible for the Laco and Bifidobacteria species to return from zero growth?
    Thanks for all your great work.

  14. I have Hashimoto’s and have been on the same dosage of Levothroid for 10 years. After reading your article on selenium, I started eating 1-2 Brazil nuts a day and a few months later had to drop my dosage. Cool, huh?

    Taking Femdophilus (Jarrow) probiotic seems to work well for me. It has L. reuteri and L. rhamnosus, among others.

  15. Chris, To your knowledge, is there a connection between Enlarged Thyroid (Goiter) and Uterine Fibroids. May 2015, I had a biopsy of both in the same week (both came back negative).
    Cancelled the recommended (scheduled) Full Hysterectomy… the
    OB-GYN not impressed/happy!
    When I mentioned to the Endocrinologist that I was also having a fibroid biopsy, he didn’t even comment. I don’t get it, as I see both conditions being related to the Endocrine (Hormonal) System. The Gynaecologist didn’t make any connection either.

    • Hi Judy-
      I have thought the same thing. In 2012 I had an endometrial cyst removed and I asked my Gynecologist if this has any correlation with my Thyroid. He said “nope” What prompted me to ask this question is are two things ;family history of Thyroid disease (at the age of 40 my grandmother had a Hysterectomy). And the attached links-see below
      Fast forward to 2014, all with in one week I was FINALLY diagnosed with Hashimoto and Thyroid cancer. I say finally because since 2012 I felt the symptoms of a dysfunctional thyroid but had always tested in the “normal” range (2.0-2.5). Even at the time of being diagnosed with Hashimoto my TSH was considered normal.

    • HI Judy, I thing we re on to something here. I had 14 uterine fibroids removed this November by myomectomy. I’m 34 and hoping to get pregnant this year. However, 3 months after the surgery 4 small new fibroids had regrown and simultaneously my blood tests revealed hyperthyroid. I’m being tested this week for graves disease, but my endo dr doesn’t think its related. My groom and I have been eating Paleo since May. We have increased our intake of fermented food and occasionaly supplementing with probiotics. I feel like wea re as healthy as we have ever been, but still having these pathologies come up is frustrating. I have been writing a blog about my experiences if you want to read. We are going to continue to search for answers and solutions.

    • Hi Judy, Extremely interesting and i believe evrything is linked as very similar to i.
      Feb 2015 diagonised with hyperthyroidism, come October 2015, massive fibroids with an external one that grew to the size of being 22 weeks pregnant, due to age (51) i have had a complete hysterectomy for it appeared sinister. With 7 weeks off work i have been trying to research and believe i have to get off my thyroid medication. I have found a way, linking it to the gut and using a naturopath. Vicki

      • I am at my wits end as to what to do next. Any advice would be greatly appreciated. I am getting to the stage where i just want to give up.
        Beginning of 2012 my abdomen suddenly became very distended and i literally looked like i was 9 months pregnant. My waist measurement went from 28 to 38 virtually overnight and stayed like that for the next 3 years (it is still not normal but is now the least of my problems) I put on 10 kilos in weight without changing my diet and I have always had a small appetite. Anyway at the same time i found digesting food painful and food would sit in my stomach for up to 8 hours after eating. End of 2012 I Had an ultrasound which as well as finding gallstones also showed a fibroid of 5cm and a massive amount of gas in my abdomen. Blood tests showed that i had both b12 and iron anaemia and very high chloresterol. I had my gallbladder removed mid 2014 but my abdomen didnt go down and at the same time my periods became very heavy and painful. Another scan showed the fibroid had grown to the size of a grapefruit so had a hysterectomy at the end of 2014. Still my abdomen remained huge and by this time I felt so poorly that I could barely function. Joints very painful (especially hips, sometimes needing crutches to walk) chronic fatigue, brain fog etc etc. 3 thyroid function tests came back normal then a doctor in spain scanned my thyroid and said the gland was massive although no external swelling and had many nodules. Next thyroid test showed my thyroid was very overactive. Started taking carbimazole last november and last weeks test showed my levels are now normal. I still have problems digesting food and am about to have a second endoscopy (the first showed inflammation with no explaination). I now give myself b12 injection every 3 months and am waiting result of a blood test for celiacs. In the last month I have had cellulitis in my nose! shingles and now a sinus and chest infection which just wont go ( darent take antibiotics as they play havoc with my digestive system) I am so tired of being passed around different consultants who do Test after test. All of them refuse to consider that all my problems may be linked. I have always believed that they are as prior to 2012 i was very fit and healthy. These days i barely feel alive most of the time and I am praying that someone out there might just be able to help me on to the path of at least feeling somewhere near normal instead of a freak.

  16. I appreciate you pointing out the study showing the huge correlation between SIBO and patients with hypothyroidism, and it is certainly something I think that is under appreciated by most physicians.

    SIBO in general seems to be widely ignored, even by many gastroenterologists.

    I would also point out that for many people with thyroid problems it will be very difficult to treat the gut without first addressing thyroid replacement (if necessary). Thyroid hormone itself can cause issues with intestinal motility and HCL levels perpetuating many common gut imbalances (SIBO and intestinal dysbiosis come to mind).

    I think the better and more efficient approach is to treat both simultaneously (whenever possible).

    As always, great and informative article.

    • I am hyperthyroid but I still have SIBO so my fast thyroid has not sped up my motility at all. Fixing the malabsorption of nutrients and fats I believe is the key to helping the thyroid but if the bacteria/organisms are eating my nutrients then will supplements even help, I don’t know. So far no supplements have really helped.

      • After multiple SIBO treatments (rifaximin and herbal antibiotics/antifungals) with success that didn’t last even for 1 week I went high fat, low carb and no grains for 6 months. My digestion and SIBO worsened so much that I was at a loss! I didn’t know what to eat anymore. Then I heard that sufficient bile was necessary for SIBO control, motility and of course- fat absorption. Since my symptoms worsened after increase in fat consumption it was logical to assume that I had problems with bile (either genetic or liver congestion) So I tried lecithin, 10g a day. Lecithin is a component of bile and when you supplement with it it makes bile flow easier. Plus it might actually emulsify fats on the spot, that is your stomach and small intestine. (not sure about this one) Anyway, I couldn’t believe the improvement in motility and digestion. Try it. If it works for you you will find out in 2-3 days.
        I am going to do a liver cleanse since I do have problems with it. I get pains on the right side ever since I overdosed on vitamin A 5 years ago. Inflammation due to vit A toxicity probably thickened my bile and congested the ducts. Regardless of what some people say about liver flush (that it’s just emulsified oil and not the actual stones) people do feel better after it. So I am gonna try.

  17. My 32 year old granddaughter who is type 1 diabetic for 5yrs. Has gastroparesis off an on for a year, in the ER and hospital about 3 times a month. Has all test except endoscopy will have in May. Could all the Reglan and narcotics have cause more problems? She needs a healthy gut yes?

  18. We all have good pertinent questions, I myself have been taking multiple bacteriocidal herbs and antibiotics for high hydrogen an methane SIBO, with long standing Candida overgrowth, and it’s very difficult to navigate and know when to go to the next step, and what it is, when you have a career, kids….life.
    I gets real complicated, and it appears nobody is minding this store and giving answers.
    Good luck.

    • Chris, are lactobacillus really supposed to be there? Isn’t lactobacillus acidophilus a firmicute? Don’t we seek for more bacteroids? Is lactibacillus able to start a cascade “good” bugs colonization?

      • Humans have for a very long time consumed foods preserved by lactofermentation whether it was on purpose or by accident. Refrigeration is only a very modern convenience. It only stands to reason that this particular type of bacteria, present on almost everything in nature, works harmoniously with our physiology.

      • Yes, lactobacillus is definitely supposed to be there—at least in most human guts that have been studied.

  19. I have a question about the thyroid and health. I had a growth on my thyroid and had to have the entire thyroid removed. How does this affect my overall health and ability to lose weight?

    • Presuming you are taking thyroid hormone and maintaining levels in the normal range, it may not have a significant impact. But if you have Hashimoto’s or another autoimmune thyroid condition, it’s possible that the body is still mounting an attack against the small amount of remaining thyroid tissue (thyroidectomy does not typically remove 100% of the tissue because of the risk of damaging other structures in that area).

      • Chris, my mum had her goiter removed before I was born, can that be the most likely cause/reason I have hypothyroidism?

  20. Chris what’s your take on the view that If you fix thyroid the body will naturally fix the gut – and that probiotics and fermented foods are unnecessary and even contraindicated for many with gut issues?

    • You could just as soon say it the other way around: fix the gut and that will take care of the thyroid. The reality is these relationships are bi-directional, and both systems will likely need to be addressed for healing to occur.

      • My reply would apply here. I have been Hypothyroid Hashimotos for years with other autoimmune issues. My thyroid dose kept going up because I could never get it under to control. I developed massive fibroids over many years and finally had a total hysterectomy 1.5 years ago. At the same time I went full on with a paleo/AIP diet. My thyroid meds were 250mg of Synthroid and 3mcg of Liothyronine prior to hysterectomy/diet. Now 1.5 years after both I am down to 125mg of Synthroid. Hormone and gut balance is huge!

  21. Chris,
    This information makes a case for my experience.
    All within a 4 month span I was diagnosed with hashimoto,papillary thyroid cancer,total thyroidectomy and radiation.
    In order for me to prepare for the radiation uptake I had to be off my Levothroxine for four weeks and avoide iodine in my diet. Pretty much consisted of a Paleo diet. Because as you know iodine is in everything. My endocrinologist informed me that I would feel “poopy” (tired and sluggish) and advised that I take the last week off from work during the 4 week withdrawal. I never felt “poopy” I felt great! I attribute this to the food that my body had been desiring all this time and truly a time to heal.
    I was that person whose thyroid panel never indicated an issue. I had my thyroid checked regularly due to my mother,grandmother and aunts all dealing with various forms of a dysfunctional thyroid. Although it always fell in the 2.0-2.5 range the docs passed as all good. However my symptoms told me otherwise. And I knew in the back of my head all was not well.
    What is your recommendation for someone who had their thyroid removed?

    • To get your thyroid hormone levels into the normal range using replacement hormone. That’s the best you can do when your thyroid has been removed.

  22. Chris, I had an allergic reaction to shell fish about 20 years and since then I have been on synthroid. Is it possible to restart your thyroid?

  23. Thank you Chris for the very informative article. I did know about the connection between thyroid dysfunction and gut flora imbalance because of the books I’ve read and the webinars I’ve listened to. In my own health journey I noticed low thyroid symptoms long before I had SIBO or even knew what it was. I did suffer with constipation, but that is also a symptom of Hashimoto’s. I learned the hard way that SIBO is contraindicated for fermented vegetables with their lacto and bifido strains. I have found that I can tolerate Prescript Assist soil organisms for probiotics, but that means I am missing all the benefits of fermented vegetable strains. I also used MEGASporebiotic but stopped as I’m pretty certain it has a corn derivative as a filler since it doesn’t say corn free on the label. The other thing I learned the hard way is that bone broth may be counterproductive for healing the gut. I drank one cup of homemade bone broth per day for a year and a half when I was using Sarah Ballantyne’s Autoimmune Paleo Food Protocol. I learned from a Cyrex Labs Array 10 blood test last fall that I am now making antibodies to gelatin, which is supposed to be healing for the gut. I learned recently that it is a protein in the bone broth that is troublesome and that meat broth is a safer way to heal the gut. I am about to embark on The Autoimmune Solution approach by Dr. Amy Myers, which will address the SIBO and heal the gut simultaneously. I sure hope this is the ticket to getting the Hashimoto’s into remission. Thank you so much for helping those of us who so desperately want to feel better.

    • Vernie,
      I am confused about the bone broth statement. Everything I read says that it is a major component to healing a leaky gut. I have been drinking it and following an autoimmune protocol (started with Amy Myers) for over a year. I feel fantastic. I do have a low thyroid (diagnosed recently) but think the broth helped heal my gut or close to it. No foods bother me anymore! I am still going to be tested this week for SIBO and parasites to be sure nothing else is stopping me from healing.

  24. Yes, my thyroid symptoms have been alleviated by healing my leaky gut. My thyroid numbers were’t awful, but I had just about every symptom of hypothyroidism and tested positive for food sensitivities to dairy, eggs, almonds. Though I was not a junk food eater, I was having almonds, almond milk, eggs and yogurt. By eliminating those foods, adding in bone broth daily and going on a low carb high fat diet, now adding in carbs like sweet potato and other fermentable foods along with some supplements, after a year, I can feel that my gut is healing. My thyroid symptoms are receding, my extra weight just fell away, my hair is growing back and my energy is returning. My thyroid numbers are also better.

    PS I did not have SIBO

  25. How do you reccommend balancing feeding the bacteria in your large intestine with pre-biotics, but not over-feeding the ones in the small intestine when you have SIBO. My experience is showing my that my SIBO is causing hypothyroidism. It seems like a tricky thing to get gut health while starving other bacteria. (and I’ve been taking Xifaxin and botanicals). Maybe one day medicine will advance enough that we can have daily feedback on how things are in the gut, and we can respond accordingly.

    • I have a similar question:

      How do you know when to feed the bacteria in your large intestine with prebiotics, when you are trying to avoid fermentable fibers in the small intestine when you have SIBO?

      • You either treat the SIBO first, and then do prebiotics later, or you can introduce prebiotics via rectal enema implant.

    • I have SIBO as well, and I added in resistant starch for easy prebiotics and I’ve definitely noticed good change. From what I’ve read, the resistant starch is great because the bacteria feed off of it, but it’s not fully digested, so it “sweeps” the small intestine on its way to the large intestine. Potato starch and plantains are good sources.

  26. I am a newbie to this, but I started with acid reflux about a year ago, then extreme fatigue, nausea, tested positive for SIBO and high TSH, ended up in the hospital for diverticultis infection at the same time. Had antiobiotics when released from the hospital, now I have physical anxiety, nausea, less acid reflux but abdominal pain, heartburn and constipation.

    I’m trying to figure out what is causing what. I’m getting retested for SIBO because it’s believed the antibiotics I had might have gotten rid of it. I am also on Synthroid which has given me more energy. I couldn’t eat fermented foods for a long time due to acid reflux but I am able to now. I also take probiotics and as much bone broth as possible. I will be tested soon again for thyroid. This is all following five years of chronic pain from a sports injury that messed up my alignment and my brain from knowing how to use my muscles.

  27. Hi Chris,
    I was diagnosed with hypothyroidism in 2012. After two years of seeing an internist every 3 months and trying every thyroid medication available at ever increasing dosages, nothing was improving my symptoms or blood test results. I bought your book after finding your name searching the internet. You seemed to be one of the only non-militant, reasonable, flexible, and non-crazy authorities out there. You were one of the only people ever to explain the whys and complexity of auto-immune conditions. There is no one solution that fits everyone. I cut coffee, corn, all grains, and sugar. I started eating liver, selenium rich foods, plantains (my go to for carbs), and making my own broth. Within 3 months of this dietrary change, I had the best blood test results during my two years of struggle with this frustrating condition and frustrating interactions with many doctor visits. My TSH finally went below 4.5 after remaining between 6-10 with all the hypothyroid/hyperthyroid symptoms in between dosage changes; I was also stretching out the remaining synthroid I had until I could see a new doctor. At that point, I had nothing to lose by trying your reasonable and sound advice. No medication including all forms of t4 and dosages, combos of t4 and t3 (hate t3!! for me) did any good for me alone. The diet and a small dosage of synthroid did the trick. My hair grew back. I sleep better. The tingling in my hands and feet disappeared. Joint pain disappeared. Brain fog disappeared. Mood swings disappeared. I’ve been on this diet for 18 months now and will never go off it if I have to feel the way I did two years ago and worry about being bald. So thank you! thank you! thank you! I’ve passed your name and book onto many others who ask about auto-immune conditions and how to improve symptoms.

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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.

  33. 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.

  34. 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).

  35. 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.

  36. 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.

  37. 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.

  38. 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.

  39. 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.

  40. 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.

  41. 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.

  42. 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

  43. 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?

  44. 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

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