Using Enzymes to Overcome Hashimoto’s


“Bad digestion is at the root of all evil,” said Hippocrates, the ancient Greek physician who is considered to be the father of modern medicine. Although he was born in 460 BC, I think he was onto something!

People with Hashimoto’s usually have a combination of nutrient deficienciesfood sensitivitiesadrenal dysfunctiongut infections, and an impaired ability to get rid of toxins. This Hashimoto’s vicious cycle of events causes an immune system imbalance which leads to the autoimmune destruction of our little thyroid gland.

An enzyme deficiency can, directly and indirectly, contribute to thyroid symptoms and autoimmunity.

Using enzymes can help with overcoming symptoms of Hashimoto’s including fatiguehair loss, nutrient deficiencies, infections, and food sensitivities as well as reducing thyroid antibodies.

There are 6 different types of enzymes that may be especially beneficial for Hashimoto’s:

  1. Protein digestive enzymes
  2. Systemic enzymes
  3. Fat digestive enzymes
  4. Broad spectrum enzymes
  5. Veggie enzymes
  6. Gluten/dairy digestive enzymes

1. Betaine with Pepsin

Studies have found that people with Hashimoto’s and hypothyroidism have low stomach acid. Low stomach acid makes it more difficult to digest our proteins, making us more tired as digestion is one of the biggest energy-requiring processes of our bodies. Additionally, when proteins are poorly digested we are more likely to become sensitive to them, and thus many people with Hashimoto’s will be sensitive to gluten, dairy, and soy (at least). This is because these proteins are amongst the most difficult to digest and are also the most commonly eaten proteins in the standard western diet.

People will develop IgG antibodies to the various proteins which are also the same types of antibodies that target the thyroid gland in autoimmune disease. When someone continues to eat these proteins, the immune system attack becomes upregulated as the influx of poorly digested proteins triggers the immune system to make more of these types of antibodies. While simply eliminating reactive proteins can help a person to feel much better and downregulate the autoimmune attack, continuing to have low stomach acid may contribute to developing new food sensitivities to proteins that are found in grains, eggs, nuts, and seeds.

If that wasn’t bad enough, the poorly digested proteins become “food” for the opportunistic bacteria that live in our gut. The gut is a delicate environment of probiotic (beneficial) and opportunistic (potentially problematic) bacteria. An overgrowth of opportunistic bacteria has been linked to autoimmunity.

Additionally, having low stomach acid makes us more susceptible to acquiring gut infections like H. pylori, Yersinia, and parasites, which can be potential root causes of autoimmunity.

While the lay press would have you believe that parasites are helpful for autoimmunity due to the positive effects of using whipworm to modulate the immune system, just like there can be probiotic and pathogenic bacteria, all parasites are not created equally! There are beneficial parasites as well as detrimental ones. Numerous parasites such as giardia, E. histolytica, Blastocystis hominis, among others, have been found to cause intestinal permeability (aka leaky gut) which leads to an immune system dysfunction that is present in autoimmune disease.

The low stomach acid can result from a nutrient deficiency, such as thiamin or B12, and can contribute to low iron levels and anemia, as we need stomach acid to extract B12 and iron from our protein-containing foods. This leads to a vicious cycle that results in hair loss, fatigue, food sensitivities, etc. Many people have been able to improve their levels of ferritin and B12 through improving their stomach acid and vice versa.

Using Betaine with Pepsin with protein-containing meals can help with getting your energy back.

Discovering the connection between my deficiency of stomach acid and Hashimoto’s was an “AHA” moment for me. After beginning to take Betaine with Pepsin with my protein containing meals, my 10-year long debilitating fatigue was lifted practically overnight! I went from sleeping for 11-12 hours per night to 8 hours — just because I started digesting my foods better! Finally, having enough energy gave me the confidence that I could overcome Hashimoto’s and my long list of health struggles.

I started writing my book about overcoming Hashimoto’s the morning after I took the right dose of Betaine with Pepsin. The restored energy gave me hope that I would be able to devote myself to research and find the root cause of my condition and that I would be able to share my knowledge to help others.

For full instructions on how to use Betaine with Pepsin, as well as alternative ways to increase your stomach acid if you don’t want to take a supplement, you can download my Low Stomach Acid Quick Start Guide.

2. Systemic Enzymes

Systemic enzymes are also known as proteolytic enzymes and act as natural immune modulators, bringing our immune system into balance. Systemic enzymes are a blend of plant and animal derived enzymes and may contain a mix of some of the following ingredients:

  • Bromelain (from pineapple)
  • Papain (from papaya)
  • Rutin or Rutoside trihydrate – (bioflavonoid)
  • Chymotrypsin –  (porcine)
  • Trypsin – (porcine)
  • Pancreatin – (porcine)

Systemic enzymes break down inflammatory cytokines that are seen in autoimmune disease and contain proteases that may be involved with breaking down pathogens such as bacteria and parasites. These enzymes also speed up tissue repair by reducing inflammation. Additionally, the enzymes reduce the antibodies to foods and the thyroid by breaking down circulating immune complexes that are formed in autoimmune disease.

Systemic enzymes have been studied extensively in Europe and have become a popular alternative to pain medications for arthritic disease and many inflammatory conditions.

A poster presentation from April 21-24, 2002 presented in Cannes, France found that Wobenzym, a proprietary blend of systemic enzymes, taken at a dose of 5 three times per day, showed very promising results in Hashimoto’s.

Here’s the summary of the study:

Forty people with Hashimoto’s who were taking Levothyroxine were given systemic enzymes for 3-6 months. Not only did the patients report a reduction of thyroid symptoms, but a normalization of thyroid ultrasound, a reduction in the number of inflammatory cells in the thyroid, and significant decreases in TPO and TG antibodies were seen as well.

Many patients were able to reduce their dose of levothyroxine, and some were able to discontinue their medications completely. Additionally, cholesterol profiles improved in the patients that had high cholesterol levels before starting the enzymes.

As systemic enzymes act on the immune system altogether, using them is also thought to be protective of developing future autoimmune conditions.

The key thing to remember about these enzymes is that they are not to be taken with food, rather they should be taken on an empty stomach, at least 45 minutes before a meal, or 1 ½ hours after a meal. Otherwise, they will get used up in the process of digestion instead of getting into the bloodstream to act on circulating immune complexes.

NOTE: While most labels of systemic enzymes will state to take 6 capsules daily, the dose of enzymes used in this particular study was 2.5 times higher at 5 capsules three times per day (on an empty stomach).

Experienced clinicians will use 5 capsules three times per day, with a good glass of water (at least 8 ounces or 240 ml). In some cases, even 10 capsules three times per day may be used in the acute phase to modulate the immune system effectively. The 6 capsules per day dose on the label is thought to be a maintenance dose.

The brand of systemic enzymes I have used successfully, and was used in the above-mentioned study, is the *Wobenzym brand.

*Wobenzym N is the formulation that was studied, however, I’ve also seen similar clinical benefits with Wobenzym PS.

3. Fat Digestive Enzymes

If you have issues with digesting fat —like 40-50% of people with Hashimoto’s do — you may benefit from an enzyme that aids in fat digestion. Fat malabsorption is easily overlooked by patients and practitioners alike.

Some signs and symptoms that may suggest you have an issue with digesting and absorbing dietary fats include frequent diarrhea, gas and bloating after eating, stomach pain, foul-smelling and greasy stools, weight loss, as well as a low fecal elastase test on a gut screen such as the GI-MAP test.

If you’ve had fat malabsorption for some time, you may also find that you will start to develop symptoms of fatty acid deficiency, as well as potential vitamin A, D, E, and K deficiencies.

The easiest to spot is fatty acid deficiency with symptoms such as dry hair, weight loss, eczema, depression, dry itchy/flaky skin or scalp, dandruff, oily scalp, and rashes.

Vitamin D deficiency can be identified on a lab test, and generally, if a person has been supplementing with vitamin D but is still showing deficient, I suspect fat malabsorption issues.

There are various reasons why a person may have difficulty with fat malabsorption. Some of the common ones include bile deficiency, pancreatic enzymes deficiency, liver backlog, and small intestinal bacterial overgrowth.

The supplement Liver & Gallbladder Support helps fat digestion in three different ways; supporting the liver’s ability to process fat with ingredients such as milk thistle, giving us extra bile through Ox bile, and supporting our bile flow such as dandelion, artichoke, and beet. This is something that can be a life changer if you have issues with fat malabsorption.

In some cases, people with fat malabsorption may also have exocrine pancreatic insufficiency, or a deficiency is pancreatic enzymes. In this case, I’ve found Pancreatic Enzymes from Pure Encapsulations to be very helpful. These enzymes are taken with every fat-containing meal. In about 50% of cases, I’ve seen pancreatic insufficiency resolve simply by using Pancreatic Enzymes for a few weeks to a few months; in other cases, people may need to take the enzymes long-term and do more detective work to identify why they are deficient in pancreatic enzymes.

Some potential reasons for pancreatic insufficiency may result from damaged microvilli, Celiac disease, SIBO, toxicity, stress, as well as alcohol use.

4. Broad Spectrum Digestive Enzymes

In addition to poor protein digestion, many people with Hashimoto’s may have an impaired ability to digest fiber, starch, and fat.

In the case of poor fiber absorption, many fibers of undigested vegetables may be found in the stools, and a person may feel very bloated after a high fiber meal. When someone is not properly digesting fats, they will often present with diarrhea, steatorrhea (fat in stools), cramping, bloating, and muscle cramps.

In addition to the Betaine with Pepsin, some may also find that a broad spectrum digestive enzyme may help them reduce symptoms of nutrient deficiencies and feel more energetic. I recommend Digestive Enzymes Ultra from Pure Encapsulations.

When foods aren’t properly digested, we are not going to be very effective at extracting nutrients from them. Vegetables and fruits are powerhouses for nutrients, and juicing may help with getting the nutrients to be better absorbed.

Fat is a crucial component of our diet, and fat malabsorption may lead to a deficiency of fat-soluble vitamins like A, D, E, K, as well as a fatty acid deficiency. Deficiencies in these nutrients can lead to numerous symptoms including vision problems, immune system imbalance, fragile bones, poor wound healing, easy bruising, bleeding gums, nosebleeds, dull hair, depression, skin disorders, and many other symptoms.

Some pathogens that have been tied to triggering Hashimoto’s, like Blastocystis hominis, thrive in the guts of those that have a difficult time digesting fats in lipid-coated homes or biofilms that make them impenetrable to digestive acids, immune cells, medications, and herbs.

In addition to eating a nutrient dense diet, taking vitamin, mineral, and fatty acid supplements may be required until digestion is optimized.

5. Veggie Enzymes

For those who have undigested vegetable fibers in their stool, taking an enzyme that helps to digest plant fibers may be helpful. I created Veggie Enzymes, by Rootcology, which is a vegetarian-friendly a digestive support formula. As a blend of amylase, protease, lactase, and other important enzymes, it aids in the digestion of proteins, fats, and carbohydrates. The cellulase breaks down plant cellulose, while the amylase breaks down starches to help the body digest starchy and fibrous foods like raw veggies and fruits. Taking these types of enzymes may help reduce gas and bloating after meals, as well as constipation and a feeling of fullness after eating only a small quantity of food.

6. Gluten/Dairy Digestive Enzymes

Two of the most common food sensitivities found in people with Hashimoto’s are gluten and dairy. (I know it can seem intimidating to cook or eat food without gluten and dairy, so I’ve created a 2-week Autoimmune Paleo recipe plan to get you started!) Gluten (the main reactive protein found in wheat), and casein (the main reactive protein found in dairy) are large protein molecules that may not be fully broken down in the human body and thus may be targeted by the immune system. As the antibodies to the foods are made by the same branch of the immune system (IgG branch) that makes antibodies to the thyroid, every time one of these reactive foods is consumed, there is a greater production of IgG antibodies — including the antibodies to the thyroid.

Dipeptidyl peptidase IV (DPP-IV) is a special enzyme that splits gluten into smaller fragments making it easier to digest and can be found in a combination enzyme product that also contains enzymes that break down casein, beta-lactoglobulin (whey), and lactose (milk sugar molecules found in dairy).

While these enzymes may not be enough to allow a person with Celiac disease to eat a whole bowl of pasta, the enzymes can be very helpful for those with gluten and dairy sensitivity. I use this product whenever I go out to eat and am concerned about cross contamination issues and have used it after accidental consumption of dairy/gluten.

Here’s a common scenario for eating outside the home

Me: “I follow a gluten/dairy/soy free diet. Are you able to accommodate my dietary needs?”
Cook/waiter/family member: ”Of course.”
Food comes, I try it, tastes suspicious…
Me: “Are you sure this doesn’t have dairy/gluten?”
Cook/waiter/family member: “No dairy/gluten…just cheese/butter/casein/whey/flour!”
Me: “I knew it! Glad I always keep my gluten/dairy digestive enzymes in my purse!”

I used to have severe reactions to dairy and gluten but have found that the Gluten/Dairy Digest blend of enzymes from Pure Encapsulations effectively minimize my reactions when I have accidentally consumed small amounts of dairy and gluten in the past. I still had a reaction, but instead of suffering for 2 or 3 days, I would only have problems for a couple of hours when exposed to gluten/dairy.

Have you tried enzymes? Have they made a difference in your health?

Hope that you find this information helpful on your journey in overcoming Hashimoto’s!

You can download a free Thyroid Diet Guide, 10 Thyroid friendly recipes, and the Nutrient Depletions and Digestion chapter for free by going to You will also receive occasional updates about new research, resources, giveaways and helpful information.


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