Gut-Thyroid Connection: 4 Steps for Breaking the Hashimoto’s Autoimmune Cycle


So many women are led to believe that their thyroid symptoms are in their heads! Well, guess what, ladies, it’s not in your head – but your thyroid troubles could be starting in your gut!

Let me tell you about one of my patients.

Karen had a life-long history of terrible bloating and constipation. Aside from this, she’d always been happy and energetic.

Soon after she turned 36, everything changed.

She started feeling exhausted all the time and became so depressed that some days she barely had enough energy and motivation to take care of her kids or make it though a whole workday. In fact, she had to switch her job to part-time just to cope, but this had an impact on her income and self-esteem, which only added to her depression.

Karen sent me a photograph of her belly when it was bloated. She was often asked if she was pregnant and indeed, I’d have thought she was 7 months pregnant from the photo – her distended belly stood out in start contrast to her otherwise tall, slim figure.

She came in for an appointment.

Given her fatigue, I ran tests for thyroid problems. Her results clearly showed Hashimoto’s disease, an autoimmune hypothyroid disorder responsible for 80% of all hypothyroid cases in the US.

But this is not the only thing testing revealed. An endoscopy revealed celiac disease.

Karen immediately removed all gluten from her diet, and within just a few weeks began noticing improvements in her digestion, energy, and mood. She decided to continue working on her diet and healing her gut and systemic inflammation before starting thyroid medication. About 2 months later, her TSH had almost normalized, and her thyroid antibodies were coming down. Her energy continued to improve, as did her mood.

Karen has remained strictly gluten free. Her thyroid function completely normalized – and here’s the amazing thing: she never did start thyroid medication.

What is the Gut –Thyroid Connection?

Hashimoto’s disease is an organ specific autoimmune disease – meaning it affects the thyroid. But at its core, it is rooted in inflammation that may begin outside of the thyroid in a substantial number of cases . One of the most common sources of inflammation that eventually leads to autoimmune conditions is intestinal hyperpermeability, or “leaky gut.”

The main job of the intestinal mucosa (the lining of the intestine) is to act as like customs officer at a border crossing. It allows nutrients from our food to pass into the submucosa where it can be assimilated for our benefit, while keeping potentially harmful proteins from our food and fragments of both healthy and harmful bacteria out of the submucosa where they can trigger inflammatory and immune reactions. Over time, persistent exposure of the submucosa to inflammatory and immune triggers causes the body to produce antibodies, special proteins that recognize and fight viruses and bacteria. These antibodies can also start to recognize and attack your body tissue, including your thyroid tissue, and sabotage your thyroid’s ability to produce or use thyroid hormones, resulting in Hashimoto’s disease.

Further, the health of the intestinal microbiome regulates overall inflammation in your body by inhibiting the production of pro-inflammatory cytokines including tumor-necrosis factor (TNF), interleukin 6 (IL-6), and nuclear factor-kappa B (NF-KB), while promoting anti-inflammatory cytokines like interleukin-10 (IL-10).

New research also suggests that there is direct cross-talk between proteins and hormones in the gut and the hypothalamic-pituitary-thyroid axis (HPT), adding yet another layer of the connection to what goes on in the gut and the health of the thyroid.

Antibiotic use, frequent use of NSAIDS (ibuprofen, Aleve, Motrin, etc.), a diet high in sugar and low in a wide variety of vegetables, over-exercise and chronic stress, all affect the health of the intestinal mucosa and the microbiome, and can determine whether you develop hypothyroidism.

Celiac disease, as in Karen’s case, creates an extreme set-up for leaky gut. In fact, as many as 10% of patients with celiac disease have hypothyroidism. But much milder forms of leaky gut and dysbiosis – which affect millions more people that has previously been recognized – can also create the environment for Hashimoto’s to develop.

The tricky thing is that not not everyone with gut problems has classic digestive symptoms. Sometimes the only symptom of gut problems is an autoimmune disease! So if you have Hashimoto’s disease, it is worth including gut healing as part of your plan.

The Core Solution: Healing the Gut-Thyroid Connection

While the gut is not the only source of autoimmune hypothyroidism, healing the gut is one of the core solutions for preventing and healing from Hashimoto’s in many cases, and can prevent further autoimmune disease from starting.

Complete gut healing can take time – even a year – but it’s not too complicated with this simple plan of action. Results often start to happen quickly, so you can feel improvement in your digestion, energy, mental clarity, and so many other areas of your life in as short as 10-30 days if you’re on the right track. I’ve seen this happen for my patients time and again.

As your overall inflammation starts to go down, your thyroid antibody numbers will also decrease. It takes at least several months and even a year to see a substantial change in antibody levels, but if you’re getting to the root of the problem, you should see a change.

Now not everyone who has Hashimoto’s can avoid or go off of thyroid medication – sometimes it remains necessary – but taking the approach of healing the underlying gut problem will prevent further health problems from arising, relieves many general symptoms, and may allow you to eventually reduce your thyroid medication dose. As inflammation resolves, so will weight loss, brain fog, sleep problems, and many other chronic symptoms many of us just assume are normal and live with.

4 Steps for Breaking the Gut-Thyroid Autoimmunity Cycle

Healing the gut is a 4-part process.


I generally recommend doing these 4 steps at the same time, but they can be done sequentially, in the order they appear here:

  1. Remove leaky gut triggers: The most common leaky gut triggers are gluten containing foods, gluten cross reactive foods (corn, coffee) and dairy products, as well as antibiotics, proton pump inhibitors (i.e., Prilosec and many other medications for reflux, and ibuprofen and other NSAIDS including Aleve, Motrin, etc.). To truly heal your gut enough to have an impact on Hashimoto’s, you will want to remove these food triggers for at least 6 months. If there’s even a hint that you are gluten intolerant, then remove gluten and gluten cross-reactive foods permanently. Speak with your doctor about whether you must be on the above medications, and whether alternatives might be possible. The same herbal supplements that help remove inflammation in the digestive system, for example, ginger and turmeric, are effective for pain, and DGL licorice has been used effectively for acid reflux, along with avoiding reflux dietary triggers and eating too close to going to bed.
  2. Replace: Take a digestive enzyme (usually 1-2 capsules with each meal) and betaine HCl (check with your doctor first if you have ulcers, a usual dose is 1-4 capsules with meals, depending on the product)) with each meal to help your body break down proteins more completely so they don’t continue to act as an immune trigger.
  3. Re-inoculate: Take a daily probiotic that includes Saccharomyces boulardii, as well as a variety of Lactobacillus and Bifidobacterium strains. Start with a low dose, usually 1 capsule per day, and increase up to 2-4 caspules per day, depending on the package instructions for the brand you purchase. And add lacto-fermented vegetables to your daily diet. If you have a major problem with gas, bloating, or a history of constipation or diarrhea, or if you notice that your digestive symptoms worsen when you start taking the probiotic, either back down on the dose or treat dysbiosis first. You may need additional help clearing out overgrowth of problematic gut flora by taking an herbal combination that contains garlic, oregano oil, or other antimicrobial herbs, for example, those that contain the ingredient berberine, like goldenseal and goldthread. Para-Shield by Gaia Herbs, Candibactin-AR and Candibactin-BR by Metagenics are examples of products that are effective for this.
  4. Repair: A number of herbs and supplements are beneficial for relieving inflammation in your gut lining, while healing the intestinal tissue. These include a daily combination of the following for 3-12 months: curcumin (1000 mg twice daily), ginger root (500-1000 mg twice daily), zinc carnosine (30 mg 1-2 times daily), L-glutamine (up to 5 gm twice daily), and marshmallow root herb, chamomile, and others which can be found in products such as Intestinal Soother or Inflamma Response by Herb Pharm. GI Benefits from DaVinci Laboratories also includes many of the ingredients in this repair section, all in one product, though it does contain stevia which I’m not a huge fan of and fruit powders for flavor which might be a trigger for gas and bloating if you have fructose intolerance.

I hope this article gives you peace of mind and freedom from thyroid troubles!


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