The Importance of Gut Health


What if I told you that the persistent bloating and stomach pain you’re experiencing could be your greatest ally on your road to recovery?

I’ve personally come a long way on my journey with Hashimoto’s over the years and hope to never return to the days when I was experiencing a long list of symptoms, including digestive problems, exhaustion, hair loss, brain fog, and anxiety. For years, I had no idea what was going on in my body, and even after my Hashimoto’s diagnosis, the long journey ahead of me toward recovery seemed daunting. Once I began to discover the connection between the gut and my Hashimoto’s diagnosis, however, I realized that I had an important key in my hands to unlocking my own remission.

While I was suffering from constant bloating, stomach pain, irritable bowel syndrome (IBS) and acid reflux, it was hard to imagine that any of those symptoms were doing me any good. But as I dove deeper into trying to uncover the mystery of these symptoms and a host of others that included exhaustion, hair loss, brain fog, and carpal tunnel, I learned to view them as a very important clue.

In my research, I came across the work of Dr. Alessio Fasano, a physician and researcher whose work has uncovered the idea that all autoimmune conditions, Hashimoto’s included, involve some degree of intestinal permeability, also referred to as “leaky gut”. His research led him to discover the three-legged stool of autoimmunity that has revolutionized the way we understand autoimmune disease.

The three legs consist of:

  1. Genetic predisposition
  2. A triggering event
  3. Intestinal permeability

I think we can all agree that we have no control over our genes, and identifying triggering event(s) that initiated your thyroid condition might take quite a bit of time and effort. But addressing leaky gut gives us an actionable pathway to begin healing and puts the power back in our hands, so we can begin the journey toward remission.

The Thyroid-Gut Connection

In the areas of natural and functional medicine, there is a widely held understanding that all disease (and thereby all healing) begins in the gut. And for good reason!

The gut performs the all-important role of digesting and absorbing the nutrients we take in, but it is also responsible for helping the immune system recognize foreign invaders from self-antigens, thereby facilitating the control of pathogens and preventing autoimmune reactions.

Interestingly, the fetal origin of the thyroid gland is the same as the stomach, digestive tract, and tongue. Because of this shared cellular origin, it would seem to make sense that improving digestive function often leads to a significant improvement in thyroid symptoms. This is encouraging news for those experiencing gut and thyroid issues!

While not everyone dealing with Hashimoto’s or leaky gut will experience bloating, stomach pains, irritable bowel syndrome and acid reflux like I did, most people with Hashimoto’s do have some degree of intestinal permeability. Even those who have no apparent gut symptoms may be experiencing intestinal permeability, and for anyone living with an autoimmune condition, addressing gut function might be the best place to start to bring healing to the body.

If we can reverse leaky gut, we can prevent or reverse autoimmunity.

What is Leaky Gut?

When functioning as they are designed to function, our healthy human intestines serve the role as both a barrier and a filter. A layer of cells form a mucus barrier, consisting of intercellular tight junctions similar to thread fibers that come together to form a piece of cloth. The intestines open and close their tight little junctions to allow nutrients to be absorbed from the food that passes through our gut and blocks the absorption of toxins like partially digested food, pollen, feces, dead cells, and bacteria that we certainly don’t want circulating around our bodies.

But what happens when those intestinal tight junctions become damaged and loose?

Those toxic substances become absorbed into the bloodstream, causing the body to recognize them as foreign invaders. This causes inflammation in the body as it begins to attack the intruders, and eventually leads to autoimmunity.

There are numerous factors that can cause intestinal permeability, and discovering which trigger (or triggers) is damaging your gut is key to restoring its function. These factors include:

How Do We Reverse Leaky Gut?

This long list of potential triggers can seem daunting, but the most common triggers that cause leaky gut are stress, food sensitivities, nutrient deficiencies, a deficiency in digestive enzymes, an imbalance of gut bacteria, and intestinal infections (including SIBO).

By addressing and managing stress and then tackling potential gut irritants, we can oftentimes reverse leaky gut and stop autoimmunity in its tracks!

There are four steps to removing some of the triggers and putting an end to leaky gut and its symptoms.

Step 1: Remove Reactive Foods

In some conditions, a single food can act as a trigger and induce intestinal permeability. This is the case with gluten (a protein found in wheat, barley and rye) and Celiac disease. Dr. Fasano estimates that for up to 20 percent of people with autoimmune conditions, the trigger may be gluten, and removing gluten will reverse the autoimmunity.

Even in a person without Celiac disease or any apparent gluten sensitivity, gluten can lead to a leaky gut because it is a protein that is difficult to digest for humans. While some people with Hashimoto’s go into remission just by removing gluten from their diet, others will need to search for additional “root causes”. These additional food sensitivities are likely to include dairy, soy, and grains, but might also include nuts, seeds, eggs or nightshades (potatoes, tomatoes, bell peppers and eggplant). The Autoimmune Paleo diet can be helpful with this.

I suggest that to discover the food triggers that are causing your leaky gut, begin by eliminating gluten, dairy, soy and grains for a period of 4 weeks. If you begin to feel a relief of gut symptoms after that trial period, you can slowly add each food group back into your diet, one at a time, allowing a few days between foods to see if you get a reaction.

If after eliminating each of these food groups you are still experiencing gut symptoms, it might be time to eliminate a wider group of possible food irritants.

This elimination diet would exclude:

  • Caffeine
  • Dairy
  • Eggs
  • Grains
  • Legumes
  • Nightshades
  • Nuts
  • Seaweed
  • Seeds
  • Sugar

It might seem extreme at first glance, but there are still many different delicious and healing foods you can eat while eliminating those that are causing your body harm.

Step 2: Supplement with Enzymes

Several studies have found that people with Hashimoto’s and hypothyroidism often have a deficiency in hydrochloric acid, resulting in low levels or even a complete absence of stomach acid.

Digestion is one of the biggest energy-requiring processes of our bodies. When extra effort is required to break down the proteins we eat, it takes a huge toll on our bodies and can often lead to extreme fatigue – a common symptom for those dealing with thyroid and other autoimmune conditions.

A digestive system that is weakened by difficulty with digesting proteins can set off a chain reaction of greater digestive trouble as it struggles to digest the more complex protein molecules found in gluten, dairy and soy. When proteins are poorly digested, we are more likely to become sensitive to them, leading many people with Hashimoto’s to become sensitive to gluten, dairy and soy, among other foods.

It’s a vicious cycle, but one that can be slowed by supplementing with hydrochloric acid and digestive enzymes, which can assist the body in breaking down these difficult to digest proteins and improving overall intestinal function and vitality. My research and personal experience have led me to recommend a few supplements to help restore proper gut function.

1. Betaine HCL with Pepsin – When I first took Betaine HCL after struggling for a decade with debilitating fatigue, I was amazed at how my energy returned almost overnight! I no longer needed to sleep for 12 hours, and my bloating was significantly reduced. All because I was finally able to digest my food.

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. They are especially important for proper absorption of protein, calcium, B12, and iron. Taking Betaine HCL with Pepsin after every protein-containing meal can assist with digestion and greatly improve energy levels. I recommend the Betaine with Pepsin supplement by Rootcology, the brand I have personally formulated. I have also used Pure Encapsulations’ Betaine with Pepsin.

2. Proteolytic Enzymes – Also known as systemic enzymes, proteolytic enzymes can help bring our immune system back into balance by breaking down pathogens and reducing inflammation that can lead to autoimmunity. In Europe, these systemic enzymes have been studied extensively and have become a popular alternative to pain medications for many inflammatory conditions.

To help restore a leaky gut, I recommend a dose of five capsules taken three times a day on an empty stomach. Systemic Enzyme Complex by Pure Encapsulations is an excellent proteolytic supplement.

3. Fat Digestive Enzymes – Fat malabsorption is easily overlooked by patients and practitioners alike, but is a common occurrence, affecting 40 to 50 percent of people with Hashimoto’s. Some signs and symptoms of fat malabsorption include greasy, smelly, floating, light-colored stools, gas or belching after eating, diarrhea, dry skin, stomach pain, gallbladder pain (which is on the right side, under the ribs), gallstones, gallbladder removal, nausea, weight loss, hormonal imbalances, and adrenal issues. A low fecal elastase test on functional medicine stool testing can also indicate fat malabsorption.

Potential reasons why a person may have difficulty with fat malabsorption include bile deficiency, pancreatic enzymes deficiency, liver backlog, and small intestinal bacterial overgrowth (SIBO).

The Rootcology Liver & Gallbladder Support supplement can help fat digestion in three different ways: it can support the liver’s ability to process fat with milk thistle, give us extra bile via ox bile, and support our bile flow with dandelion, artichoke, and beets. If you have issues with fat malabsorption, this is life-changing support.

4. Vegetable Digestive Enzymes – Many people with Hashimoto’s may also have an impaired ability to digest vegetables due to fiber and starch content. In some cases of hypothyroidism, an indigestible ball of plant fiber material known as a phytobezoar has been found to cause bowel obstruction. In the case of poor fiber absorption, undigested vegetables fibers may be found in the stools, and high-fiber meals may cause bloating. A vegetable digestive enzyme that contains fiber-digesting enzymes like cellulase, and/or starch digesting enzymes like amylases, may help with digesting vegetables. I formulated the Rootcology Veggie Enzymes with a specific combination of enzymes, including cellulase and amylase, to help support this digestive process.

5. Broad Spectrum Digestive Enzymes – A broad spectrum digestive enzyme may also be helpful with decreasing symptoms of nutrient deficiencies and increasing energy. Broad spectrum enzymes, like Digestive Enzymes Ultra from Pure Encapsulations, promote optimal digestion of proteins, fats, andcarbohydrates. Digestive Enzymes Ultra is comprised of a mixture of vegetarian enzymes, to support enhanced digestion for optimal nutrient bioavailability and absorption.

Step 3: Balance the Gut Flora

The gut is home to trillions of bacteria, and 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. So, you can see how important it is to make sure our gut flora is well balanced.

Gut flora balance is achieved in large part through eating a wide variety of healthy foods, but for those on restrictive diets to help get to the root cause of their autoimmunity, this might be difficult. For that reason, it is often necessary to supplement with fermented foods and probiotics.

Fermented foods – Sauerkraut and similar fermented vegetables are a wonderful source of beneficial bacteria and can help to restore proper gut flora when consumed regularly. Similarly, kefir and yogurt offer an abundance of good bacteria, but should be avoided by those who have been determined to have a sensitivity to dairy. Coconut yogurt and fermented coconut water are great alternatives.

Probiotics – Widely used to rebalance gut bacteria, probiotics can be a powerful tool for those dealing with leaky gut, as they can help restore healthy gut flora by displacing the pathogenic bacteria.

It is important to note that not all probiotics are created equally, and it’s crucial to start slowly and build up from there. As the “good” bacteria begins to take up residence in your intestines and displace the “bad” bacteria, the die-off can sometimes create what’s called a Herxheimer reaction. This can include lethargy, difficulty concentrating, cravings for sweets, diarrhea, rashes, irritability, gas, bloating, headache, nausea, vomiting, congestion, and increased autoimmune symptoms. This type of reaction usually clears within three to five days and leaves the person feeling much better in the end.

There are several different types of probiotics that can be beneficial for those dealing with Hashimoto’s. Lactic acid-based probiotic recommendations include VSL#3Ther-Biotic Complete by Klaire Labs, and Probiotic 50B by Pure Encapsulations. Yeast-based probiotics are a safer option for those combating SIBO (small intestine bacterial overgrowth), in which case I recommend Saccharomyces boulardii by Pure Encapsulations.

Finally, spore-based probiotics have recently been shown to reduce allergies and asthma, in addition to helping recovery from autoimmune disease and reducing SIBO. I recommend MegaSporeBiotic.

Step 4: Nourish the Gut

Providing nourishing food and supplements is an important last step to give your gut long term support. By adding a few critical nutrients, we can both heal and help prevent leaky gut.

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 reported benefits of bone broth include boosting immunity, relieving joint pain, increasing energy, improving digestion, and giving you a more youthful appearance. Most importantly, for those suffering from leaky gut, the gelatin in bone broth actually helps to seal the junctions in the intestines so they are no longer permeable; and so that toxic substances can no longer pass through the intestinal wall.

Best of all, bone broth is cheap and easy to make and makes a delicious beverage or soup to sip any time of day.

Here’s an easy bone broth recipe that can be thrown together in a slow cooker before bed and enjoyed the next day:

Easy Bone Broth

5 chicken legs
2 cups mixed chopped carrots, onions, and celery
1 tablespoon apple cider vinegar
Sea salt to taste
Purified water

Add all ingredients to a slow cooker and cook overnight, or for 8-24 hours. You’ll wake up to a delicious smell!

Watch my Video on How to Make Bone Broth

In addition to bone broth, supplemental L-glutamine (5 g, 3 times per day), zinc (no more than 30 mg per day), NAC (1800 mg per day), omega-3 fatty acids (1-4 g per day), and Vitamin D (5000 IU per day) have nourishing properties that can assist in healing the gut lining and restoring optimal gut function.

Could an Infection Be at the Root?

In some cases, even after removing problematic foods and adding supplements, a person will still have symptoms of a leaky gut. In this case, we’ve got to look even deeper to get to the root cause, which can oftentimes be found in an underlying gut infection.

Since gut infections can lead to intestinal permeability, removing the infections can be the missing link in gut repair. It can be tricky to identify which type of infection is the culprit, but a few common ones I see in my Hashimoto’s clients include: Blastocystis hominisH. pyloriSIBO or yeast overgrowth.

If you’ve hit a plateau with your healing and are losing more foods, instead of gaining foods back after a “leaky gut protocol”, I recommend pursuing gut testing. However, all gut tests are not created equally! I personally had numerous gut tests show that I was “negative” for a gut infection before I tested positive for Blastocystis hominis, a potential Hashimoto’s trigger. My current favorite test for gut infections is the GI-MAP stool test.

I also recommend testing for SIBO. SIBO testing is done via breath testing, like the SIBO lactulose test from BioHealth. Unfortunately, current stool tests do not test for SIBO, and SIBO breath tests will not reveal infections in the stool.

For more information about identifying and treating these infections, you may wish to read the “Advanced Protocols” chapter in my book Hashimoto’s Protocol: A 90-Day Plan for Reversing Thyroid Symptoms and Getting Your Life Back.

If you discover that you do have an intestinal infection, the good news is that you now know one of the root causes of your autoimmune condition and have targeted tools to help you heal. You may need a combination of treatments that might include various types of herbs, as well as antibiotic, antifungal, antiviral or antiprotozoal agents, to eradicate these infections. Each infection will require a different approach, but please believe that with the right support, healing your gut can lead to an elimination of your gut-related symptoms—and recovery is possible!

You can find more information about the gut and thyroid connection, along with my complete healing protocol, in my book Hashimoto’s Protocol.

Also, be sure to sign up to my weekly newsletter to get a free book chapter, recipes, Thyroid Diet start guide and notifications about upcoming events and my latest research.


  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. Kvantchakhadze R. Wobenzym in the complex treatment of autoimmune thyroiditis. Int J Immunorehab. 2002;4(1):114.
  3. Liponis M, Geyer C, Hubkova T. Successful Eradication of Helicobacter pylori With Over-the-counter Products. . 2015;7(5).
  4. Mariani M, Palpacelli A, Mussoni A, Rossodivita A. Hashimoto’s thyroiditis: an accidental discovery of a lingual thyroid in a 7-year-old child. Case Reports. 2013;2013:bcr2013200247-bcr2013200247. doi:10.1136/bcr-2013-200247.
  5. Mehrdad M, Mansour-Ghanaei F, Mohammadi F, Joukar F, Dodangeh S, Mansour-Ghanaei R. Frequency of Celiac Disease in Patients with Hypothyroidism. Journal of Thyroid Research. 2012;2012:1-6. doi:10.1155/2012/201538.
  6. Mori K, Nakagawa Y, Ozaki H. Does the Gut Microbiota Trigger Hashimoto’s Thyroiditis?. Discovery Medicine. 2012;14(78):321-326.


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