I was diagnosed with Hashimoto’s after almost a decade of some strange and frustrating symptoms, including “irritable bowel syndrome,” fatigue, acid reflux, hair loss, anxiety, carpal tunnel, and countless others. I wondered if all of my symptoms were connected. My endocrinologist dismissed the idea, but it turns out he didn’t know what he didn’t know! Surprisingly, he wasn’t aware of the new research on why autoimmunity happens. Many people think of Hashimoto’s as a thyroid problem, but that’s not the whole story.
Hashimoto’s is an autoimmune disease in which the immune system mistakenly attacks the thyroid gland, leading to thyroid-related symptoms. It’s important to note that while Hashimoto’s often causes hypothyroidism, the two are not the same, as autoimmunity is the underlying cause behind Hashimoto’s.
When it comes to addressing the root cause of Hashimoto’s and autoimmune disease in general, there’s a key piece of the puzzle that we can’t overlook: the gut.
More specifically, emerging research has found that intestinal permeability (also known as leaky gut) is a driving factor behind autoimmune thyroid disease.
Everyone with autoimmunity, including those with Hashimoto’s, will experience some degree of intestinal permeability. In fact, this is one of the three factors that must be present for an autoimmune disease to develop (more on the three-legged stool of autoimmunity below).
Healing a leaky gut can be a total game-changer in putting Hashimoto’s into remission and resolving many associated symptoms.
If you’ve tried everything to manage your thyroid symptoms without seeing improvement, if you struggle with gut issues, or if you have been diagnosed with irritable bowel syndrome (IBS), you don’t want to overlook the role of intestinal permeability.
In this article, you’ll learn:
- About the three-legged stool of autoimmunity
- Signs and symptoms that you have a leaky gut
- Why leaky gut is such a crucial factor in Hashimoto’s
- How to heal intestinal permeability
The Three-Legged Stool of Autoimmunity
Dr. Alessio Fasano, world-renowned gastroenterologist and gluten intolerance expert, describes autoimmunity as a three-legged stool that needs three things to be present to manifest:[1]
- A genetic predisposition
- Intestinal permeability (leaky gut)
- Exposure to a trigger, such as trauma, stress, toxins, the use of certain medications, and/or exposure to an antigen (any substance that induces the immune system to produce antibodies against it)
When functioning as intended, our intestines serve as both a barrier and a filter. A layer of cells forms a mucus barrier, consisting of intercellular tight junctions similar to thread fibers that come together to form a piece of cloth. The intestines selectively open and close these junctions to allow nutrients to be absorbed from the food that passes through our gut, as well as block the absorption of toxins like partially digested foods, pollen, feces, dead cells, and other bacteria. [2]
When these intestinal tight junctions become damaged or loose, toxic substances can pass through into the bloodstream, causing the body to tag them as foreign invaders. This leads to inflammation in the body as it begins to attack the intruders, and eventually leads to autoimmunity. According to Dr. Fasano, every person with an autoimmune disorder has some degree of leaky gut. [3]
While we can’t change our genes, we can reverse an autoimmune condition by removing the trigger(s) that contributed to its development, and by healing intestinal permeability. (You can read more about reversing autoimmunity in this article.) When you remove one or both of these factors, the “three-legged stool” of autoimmunity will no longer be able to stand!
What does this mean for those with Hashimoto’s?
It means healing and supporting the integrity of the intestinal lining by removing dietary triggers such as food sensitivities, addressing nutrient deficiencies, restoring healthy zinc and glutamine levels, promoting healthy flora in the gut with pre- and probiotics, and addressing any gut infections.
Signs You Have Intestinal Permeability
Intestinal permeability, sometimes called “leaky gut,” can show up in many different ways, and in some cases, it doesn’t produce obvious symptoms at all.
For many people, the first clues are digestive problems such as bloating, diarrhea, constipation, abdominal pain, or patterns consistent with irritable bowel syndrome (IBS) and acid reflux/GERD. Others may notice they’ve developed new food sensitivities.
If you’ve been diagnosed with IBS, then you likely experience some (or all) of these symptoms, and there’s a good chance you have some degree of intestinal permeability. In fact, recent research has shown intestinal barrier dysfunction in a significant portion of adults and children with IBS, especially in the diarrhea-predominant (IBS-D) and post-infectious-IBS subtypes. [4]
Digestive symptoms are a major red flag that suggests you may have some level of intestinal permeability, however, many people may not have gut symptoms at all. This “silent” intestinal permeability can still cause issues, and these people may experience symptoms they don’t realize tie back to their gut, such as fatigue and brain fog, skin manifestations like acne, rashes, eczema, or hives, joint pain, and nutrient deficiencies.
For those with autoimmune conditions, including Hashimoto’s, intestinal permeability is almost always part of the picture, driving immune system activation.
It’s important to remember that some individuals may be entirely asymptomatic, which means intestinal permeability can still be present and fueling inflammation beneath the surface without producing immediate or obvious warning signs.
When I started studying functional medicine and the latest research in an attempt to get my Hashimoto’s into remission, I learned that IBS often precedes an autoimmune diagnosis by 5-10 years, and that the immune breakdown begins to occur shortly after IBS symptoms present. [5]
This was eerily consistent with my experience. I was diagnosed with IBS in 2002, and got the Hashimoto’s diagnosis 7 years later. Between the two diagnoses, I started to develop more and more symptoms. What started as diarrhea progressed to stomach pains, anxiety, then tangled hair, then multiple allergies, hives, chronic cough/GERD, joint pain, and eventually cold intolerance, brain fog, and hair loss. My path to healing Hashimoto’s was very much paved by healing my gut. Since my Hashimoto’s diagnosis over a decade ago, I have learned so much about what disrupts the gut barrier. This is why I decided to write a new book focused on gut health.
In my upcoming book, IBS: Finding and Treating the Root Cause of Irritable Bowel Syndrome, I dive deep into the root causes of irritable bowel syndrome and how to address them, so that readers can get intestinal permeability (and all of its consequences, including Hashimoto’s) into remission once and for all. This book has been over a decade in the making, and I’m so excited to share all I’ve learned (spoiler – it’s a lot, and includes root causes you probably haven’t heard of before).
Check out IBS: Finding and Treating the Root Cause of Irritable Bowel Syndrome and preorder your copy today!
Why Intestinal Permeability Matters in Hashimoto’s
As I mentioned earlier, some degree of intestinal permeability is going to be present for nearly everyone with Hashimoto’s.
When the leaky gut starts allowing food proteins (like gluten), toxins, and microbes to cross the intestinal barrier into the bloodstream, this is when we can start to see an autoimmune reaction.
These foreign substances sound the alarm, and the body’s immune system attacks these invaders. In the process, the body can sometimes get confused and start attacking itself (hence, auto-immunity). For those with Hashimoto’s, this attack is targeted toward the thyroid gland.
One of the reasons that gluten is of particular concern for those with Hashimoto’s and autoimmunity is because it’s actually been shown to produce intestinal permeability in most people (in celiac disease, the reactions are extreme and long-lasting – think weeks, while in non-celiac gluten sensitivity, the reactions may last days). [6] Additionally, because of structural similarities between gluten (specifically the gliadin protein) and the thyroid gland, the theory of molecular mimicry suggests that the immune system will mistakenly attack the thyroid gland when exposed to gluten, which can trigger or worsen autoimmune thyroid disease. [7]
This is why I suggest that everyone with Hashimoto’s eliminate gluten from their diet. In my 2015 survey of over 2,230 readers with Hashimoto’s, 88 percent of people who went gluten-free felt better! And 86 percent of people who went gluten-free reported an improvement in digestive symptoms.
Intestinal permeability and thyroid autoimmunity can also become a vicious cycle. Leaky gut fuels the autoimmune attack on the thyroid, and thyroid hormone imbalances can slow down gut motility, making us more susceptible to gut imbalances and gut infections such as small intestinal bacterial overgrowth (SIBO), which can further fuel gut permeability.
It’s important to recognize the role of gut health in Hashimoto’s, and while we may not always know the triggers for autoimmunity, we can always work on gut health. I’ve spoken about this topic in great detail in my past articles (and go into depth about it in my new IBS book which you can preorder here), but I also wanted to provide a summary of some things you can do at home to improve the health of your gut.
The 5R Approach to Healing Intestinal Permeability
1. Remove Triggers
One of the first steps I’d recommend to everyone with Hashimoto’s is to identify and remove foods that may be irritating to the gut or triggering permeability. I suggest that those with Hashimoto’s remove gluten, dairy, and soy as a starting point. These are the three most common reactive foods, and removing them can be tremendously helpful for gut and thyroid symptoms.
Some people may need to dig a little deeper for their personal food sensitivities. You can learn about other common food sensitivities for those with Hashimoto’s and how to figure out which foods you may be sensitive to in this article.
I typically recommend an elimination diet for 90 days; but I do have to warn you, a push for increasingly restrictive diets has been discussed by patient advocacy groups for some time, yet restricting more foods can be harmful for your microbiome and gut permeability if you don’t look at the full picture of gut health. For example, another big driver of intestinal permeability is gut infections. You could be eating ice cubes and nothing else, and your gut would still be permeable if you have a gut infection.
If you have not seen improvement/remission within 90 days after following the diet I described above (removing gluten, dairy, and soy), I would suggest testing for gut infections. I do go into the comprehensive testing in the IBS book, and I’ve written articles on the common infections I see in Hashimoto’s, including Blastocystis hominis, Candida, and SIBO.
2. Repair the Gut Lining
In many cases, gut permeability can be supported by healing foods, nutrients, and mucilaginous herbs.
- Bone broth: One of the easiest ways to soothe and heal the lining of the gut is to have a delicious cup of bone broth. Bone broth is a traditional food that we hear a lot about these days because it really is one of the most nourishing foods we can feed our bodies. The gelatin in bone broth actually helps to seal the junctions in the intestines so they are no longer permeable. [8] Check out my simple bone broth recipe here.
- Glutamine: Glutamine is the best-studied substance for healing intestinal permeability. Supplementation of this important amino acid has been found to reduce the leaky gut associated with the use of NSAIDs and abdominal surgery. [9] A deficiency in glutamine is also known to cause increased intestinal permeability in mouse models and malnourished children. [10] Pure Encapsulations makes an L-glutamine powder that I like.
- Zinc: Zinc plays a specific role in gut health, as deficiency has been associated with increased intestinal permeability, susceptibility to infections, and reduced detoxification of bacterial toxins. [11] In conditions such as Crohn’s disease, replenishing zinc has been shown to help repair intestinal permeability. [12] Because zinc is not stored in the body, a daily intake is recommended even for the general population, and people with Hashimoto’s and other autoimmune conditions should consider zinc supplementation as part of their everyday regimen. I often recommend zinc picolinate for proper thyroid function, but I have found that zinc carnosine is the most helpful version for gut healing.
- Mucilogenous Herbs: Mucilaginous herbs are plants rich in soothing, gel-like compounds that form when mixed with water. These herbs, such as slippery elm, marshmallow root, aloe vera, and flaxseed, coat and calm irritated tissues along the digestive tract. [13] They act almost like a natural bandage, protecting the gut lining while reducing inflammation and supporting repair. For those with conditions like IBS, reflux, or intestinal permeability, mucilaginous herbs can be especially helpful, as they not only ease discomfort but also create a more favorable environment for healing. The Rootcology Gut R&R Powder contains a mix of L-glutamine, zinc carnosine, and mucilaginous herbs. 🙂
3. Reinoculate
Refilling the microbiome with beneficial microbes can play a critical role in healing intestinal permeability. [14] Additionally, studies have shown that autoimmune disorders can be brought on by an overabundance of the wrong type of bacteria, and can be reversed by an increase in beneficial bacteria. [15]
Eating a diverse range of foods supports a healthy gut microbiome. However, during the early stages of healing, this can be difficult, as many individuals may need to eliminate certain foods. During this time, you may need to rely on external sources of beneficial flora, such as fermented foods and probiotic supplements.
Fermented Foods
Fermented foods like sauerkraut and other fermented vegetables (that are kept in the refrigerator section of the grocery store or are homemade and refrigerated) have an abundance of beneficial bacteria and can be very helpful in rebalancing the gut flora. [16]
Since I recommend avoiding dairy in Hashimoto’s, skip the yogurt and kefir, and try fermented coconut water or fermented coconut yogurt instead.
I have found that most people with Hashimoto’s can really benefit from fermented foods. However, those with small intestinal bacterial overgrowth (SIBO) may have an adverse reaction, and should steer clear of fermented foods until they’re further along in their healing journey.
Probiotics
Probiotics are widely used to rebalance the gut flora. The beneficial bacteria in probiotics help crowd out harmful microbes and restore the balance needed for healthy intestinal permeability.
I’ve found the following three types of probiotics to be helpful for people with Hashimoto’s:
- High-dose Lactobacillus: Lactobacillus-based (lactic acid) probiotics are the most commonly used and can be very helpful in rebalancing gut dysbiosis. Many people with Hashimoto’s test deficient in these probiotic bacteria on stool tests. While I recommend starting low (1 to 10 billion CFUs per day) and increasing slowly, doses of at least 50 billion CFUs per day are needed for therapeutic effect. These probiotics can be very helpful for people with Hashimoto’s, who often show low levels of them on gut lab tests. However, they may be problematic for people with SIBO, which can be caused by an overgrowth of various bacteria. If you have SIBO, consider S. boulardii instead (more information below). Rootcology ProB 50 is a high-quality option, and I have also seen benefits from Ther-Biotic Complete by Klaire Labs.
- Saccharomyces boulardii (S. boulardii): S. boulardii is a beneficial yeast that helps to raise our secretory IgA, which acts as a protective barrier in the gut, leading to the removal of opportunistic and pathogenic organisms from the gut, and preventing new infections as well as reinfections. [17] This type of probiotic is an excellent tool for addressing dysbiosis, yeast overgrowth, and parasitic infections, and it can be used concurrently with antibiotics. Furthermore, yeast-based probiotics do not have a propensity to increase SIBO. A dose of 250 mg to 2,000 mg per day of Rootcology S. Boulardii is a good starting point.
- Spore-based probiotics: Spore-based probiotics have shown promise in supporting various autoimmune diseases, as well as in reducing allergies and asthma. [18] They also have an ability to boost Lactobacillus colonies, so they can be used concurrently with Lactobacillus probiotics, as well as in place of them. Unlike Lactobacillus probiotics, spore-based probiotics can reduce SIBO and increase gut diversity by boosting the growth of other beneficial flora. [19] Rootcology’s Spore Flora contains five targeted Bacillus strains. The starting dose for spore-based probiotics is one capsule every other day, and the therapeutic dose is two capsules per day. Once the desired effect has been seen (generally three to six months in people with Hashimoto’s), I recommend dropping down to a maintenance dose of one capsule per day.
An important note on probiotics: You always want to start low and go slow. While your ultimate target may be to take three probiotics at therapeutic doses, you will only start one probiotic, at a small dose, then increase the dose of that probiotic slowly, before introducing a second probiotic, at a low dose, and so on!
There may be some initial discomfort when introducing probiotics, but it should subside within a couple of weeks (if it doesn’t, discontinue using them).
4. Replace: Digestive Enzymes
Several studies have found that people with Hashimoto’s and hypothyroidism often have a deficiency in hydrochloric acid and digestive enzymes, resulting in low levels or even a complete absence of stomach acid. [20] This affects digestion, energy levels, and nutrient absorption. It also makes us more susceptible to gut infections, which can lead to intestinal permeability.
Supplementing with the right enzymes can assist the body in breaking down difficult-to-digest proteins and improve overall intestinal function and vitality.
Here are some enzymes that will help restore gut function and integrity:
- Betaine with pepsin: Betaine HCL and pepsin are naturally occurring components of the gastric juices that break down protein bonds in our food, to make nutrients and amino acids more bioavailable. As mentioned, many people with Hashimoto’s have low stomach acid. Using a supplement such as Rootcology’s Betaine with Pepsin or Pure Encapsulations Betaine HCl Pepsin can help digest protein-containing meals. Please see my full article on betaine with pepsin for more information and dosing instructions.
- Broad-spectrum digestive enzymes: I’ve found that some individuals may need to take a variety of additional enzymes to properly restore digestion.
There are a lot of enzyme options to choose from, depending on your individual needs and symptoms (because we are all snowflakes with unique patterns). I strongly suggest reading my article on the Ultimate Guide to Enzymes, which includes assessments to help you determine which types of enzymes will be best for your unique needs.
5. Rebalance
When you remove triggering foods from your diet, start actually digesting food, and give the gut soothing foods and nutrients to repair the gut lining, you should start to see an improvement in digestive symptoms. This will be obvious to most people (hello, less bloating!), but there are also important changes going on behind the scenes that may be less obvious.
With all of these pieces in motion supporting gut permeability, the immune system will start to calm down, which can lead to reduced thyroid antibodies and improved thyroid symptoms.
This gut-immune communication is an important piece of healing intestinal permeability. The rebalance step involves finding additional factors (such as thyroid hormones) that may be out of balance and can contribute to poor gut health.
A key piece of communication is between the thyroid and the gut. Hypothyroidism often leads to slowed gut motility, which can mean constipation. Aside from the fact that constipation is uncomfortable, it can also become a real problem for gut health.
When food is not moving through the digestive system as quickly as it should, it can lead to bacterial overgrowths that can affect gut permeability.
Optimizing thyroid hormones can help normalize gut motility, and there are also many other interventions that can help get things moving. See my articles on constipation and thyroid medications for further guidance.
I will be sharing more about gut health in the next few months and what you, as someone with Hashimoto’s, can do to heal. I would also love to ask you a favor – if you have benefited from my work, and know someone with IBS, could you let them know about my upcoming book? I would love to help people solve their gut issues before they turn into autoimmune issues!
Takeaway
Hashimoto’s is not just a thyroid condition – it’s a gut condition, too. The sooner we understand that and start treating the root cause of autoimmune thyroid disease, the sooner we can get to feeling better!
Intestinal permeability is a major contributing factor to autoimmune disease, and working to heal the gut can lower inflammation, reduce autoimmune activity, and bring relief to thyroid and digestive symptoms.
If you have digestive issues that you can’t seem to quite figure out, or if you’ve been diagnosed with IBS, I highly recommend you check out my latest book, IBS: Finding and Treating the Root Cause of Irritable Bowel Syndrome and preorder your copy today!
In the meantime, following the steps above on removing reactive foods, supporting the gut lining with supplements like Rootcology’s Gut R&R, supporting digestion with enzymes and probiotics, and ensuring everything is moving properly. You can start improving digestive and thyroid symptoms sooner rather than later!
Your gut CAN heal, and with it, your thyroid.
Have you ever experienced gut permeability? What helped you heal?
As always, I wish you the very best of health!
P.S. You can also download a free Thyroid Diet Guide, 10 thyroid-friendly recipes, and the Nutrient Depletions and Digestion chapter of my first book for free by subscribing to my weekly newsletter. You will also receive occasional updates about new research, resources, giveaways, and helpful information.
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References
[1] Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol. 2012;42(1):71-78. doi:10.1007/s12016-011-8291-x
[2] Schoultz I, Keita ÅV. The Intestinal Barrier and Current Techniques for the Assessment of Gut Permeability. Cells. 2020;9(8):1909. Published 2020 Aug 17. doi:10.3390/cells9081909
[3] Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol. 2012;42(1):71-78. doi:10.1007/s12016-011-8291-x
[4] Hanning N, Edwinson AL, Ceuleers H, et al. Intestinal barrier dysfunction in irritable bowel syndrome: a systematic review. Therap Adv Gastroenterol. 2021;14:1756284821993586. Published 2021 Feb 24. doi:10.1177/1756284821993586
[5] Campbell AW. Autoimmunity and the gut. Autoimmune Dis. 2014;2014:152428. doi:10.1155/2014/152428
[6] Cenni S, Sesenna V, Boiardi G, et al. The Role of Gluten in Gastrointestinal Disorders: A Review. Nutrients. 2023;15(7):1615. Published 2023 Mar 27. doi:10.3390/nu15071615
[7] Esfahani KS, Asri N, Mahmoudi Ghehsareh M, Rezaei-Tavirani M, Jahani-Sherafat S, Rostami-Nejad M. The Role of Gluten in the Development of Autoimmune Thyroid Diseases: A Narrative Review. Int J Endocrinol Metab. 2024;22(3):e153730. Published 2024 Jul 30. doi:10.5812/ijem-153730
[8] Paray BA, Albeshr MF, Jan AT, Rather IA. Leaky Gut and Autoimmunity: An Intricate Balance in Individuals Health and the Diseased State. Int J Mol Sci. 2020;21(24):9770. Published 2020 Dec 21. doi:10.3390/ijms21249770
[9] Rao R, Samak G. Role of Glutamine in Protection of Intestinal Epithelial Tight Junctions. J Epithel Biol Pharmacol. 2012;5(Suppl 1-M7):47-54. doi:10.2174/1875044301205010047
[10] Ueno PM, Oriá RB, Maier EA, et al. Alanyl-glutamine promotes intestinal epithelial cell homeostasis in vitro and in a murine model of weanling undernutrition. Am J Physiol Gastrointest Liver Physiol. 2011;301(4):G612-G622. doi:10.1152/ajpgi.00531.2010
[11] Skrovanek S, DiGuilio K, Bailey R, et al. Zinc and gastrointestinal disease. World J Gastrointest Pathophysiol. 2014;5(4):496-513. doi:10.4291/wjgp.v5.i4.496
[12] Sturniolo GC, Di Leo V, Ferronato A, D’Odorico A, D’Incà R. Zinc supplementation tightens “leaky gut” in Crohn’s disease. Inflamm Bowel Dis. 2001;7(2):94-98. doi:10.1097/00054725-200105000-00003
[13] Dybka-Stępień K, Otlewska A, Góźdź P, Piotrowska M. The Renaissance of Plant Mucilage in Health Promotion and Industrial Applications: A Review. Nutrients. 2021;13(10):3354. Published 2021 Sep 24. doi:10.3390/nu13103354
[14] Chakaroun RM, Massier L, Kovacs P. Gut Microbiome, Intestinal Permeability, and Tissue Bacteria in Metabolic Disease: Perpetrators or Bystanders?. Nutrients. 2020;12(4):1082. Published 2020 Apr 14. doi:10.3390/nu12041082
[15] Wu HJ, Wu E. The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes. 2012;3(1):4-14. doi:10.4161/gmic.19320
[16] Leeuwendaal NK, Stanton C, O’Toole PW, Beresford TP. Fermented Foods, Health and the Gut Microbiome. Nutrients. 2022;14(7):1527. Published 2022 Apr 6. doi:10.3390/nu14071527
[17] Terciolo C, Dapoigny M, Andre F. Beneficial effects of Saccharomyces boulardii CNCM I-745 on clinical disorders associated with intestinal barrier disruption. Clin Exp Gastroenterol. 2019;12:67-82. Published 2019 Feb 11. doi:10.2147/CEG.S181590
[18] McFarlin BK, Henning AL, Bowman EM, Gary MA, Carbajal KM. Oral spore-based probiotic supplementation was associated with reduced incidence of post-prandial dietary endotoxin, triglycerides, and disease risk biomarkers. World J Gastrointest Pathophysiol. 2017;8(3):117-126. doi:10.4291/wjgp.v8.i3.117
[19] Marzorati M, Van den Abbeele P, Bubeck S, Bayne T, Krishnan K, Young A. Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME® model of the human gastrointestinal system. Food Res Int. 2021;149:110676. doi:10.1016/j.foodres.2021.110676
[20] Wiersinga WM, Touber JL. The relation between gastrin, gastric acid and thyroid function disorders. Acta Endocrinol (Copenh). 1980;95(3):341-349. doi:10.1530/acta.0.0950341
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