Dr. Izabella Wentz, PharmD, FASCP, Guest
Thyroid Nation

“Bad digestion is at the root of all evil”- said Hippocrates, the ancient Greek physician who is considered 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 deficiencies, food sensitivities, adrenal dysfunction, gut infections and an impaired ability to get rid of toxins. This vicious cycle of events causes an immune system imbalance, which leads to the autoimmune destruction of our little thyroid gland.

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An enzyme deficiency can, directly and indirectly, contribute to thyroid symptoms and autoimmunity. Using enzymes can help with overcoming symptoms of Hashimoto’s; including fatigue, hair loss, nutrient deficiencies, infections, and food sensitivities as well as reducing thyroid antibodies. There are 4 different types of enzymes that may be especially beneficial, protein digestive enzymes, systemic enzymes, broad-spectrum enzymes, and gluten/dairy digestive enzymes.


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 (in the 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 that 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 our 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 a potential root cause of autoimmunity.

Click the links to read more about Infections and 6 Common Root Causes.

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 really help with getting your energy back.  Discovering the connection between my deficiency of stomach acid and Hashimoto’s was an “A-HA” moment for me. After beginning to take Betaine with Pepsin along 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! This was over two years ago, and 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 directions on how to use this enzyme, as well as alternative ways to increase your stomach acid if you don’t want to take a supplement, you can download my free book chapter at 

The brand of Betaine with Pepsin that I used is made by a company that produces hypoallergenic supplements called Pure Encapsulations and can be viewed here.


Systemic enzymes are also know 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 also 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 to 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.

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, reduced 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 to 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, of 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 (a 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 two brands of systemic enzymes I have used successfully are the Pure Encapsulations brand as well as the Wobenzym brand (Wobenzym was the brand that was used in the above mentioned study).


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, like blastocystis hominis thrive in the guts of those that have a difficult time digesting fats in lipid-coated homes or biofilms that may 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.


Two of the most common food sensitivities found in people with Hashimoto’s are to gluten and dairy. 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 may thus 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.

Thyroid-Nation-Izabella-Wentz-AdHere’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/flour!”

Me: I knew it! Glad I always keep my Gluten/Dairy digestive enzymes in my purse!

I used to have really severe reactions to dairy and gluten, but have found the Gluten Dairy Digest blend of enzymes from Pure Encapsulations effectively minimized 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 instead have problems for a couple of hours when exposed to gluten/dairy.

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

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About the Author

Using Enzymes To Overcome Hashimoto'sDr. Izabella Wentz, PharmD, FASCP is a passionate, innovative, solution-focused pharmacist with an exceptional blend of creativity, empathy and clinical experience. 
She received the Doctor of Pharmacy Degree in 2006 from Midwestern University. She is a Fellow of the American Society of Consultant Pharmacists, and holds certifications in Medication Therapy Management as well as Advanced Diabetes Care and is also a 2013 recipient of the Excellence in Innovation Award from the Illinois Pharmacists Association. After being diagnosed with Hashimoto’s Thyroiditis in 2009, Dr. Wentz was surprised at the lack of conventional medical knowledge about lifestyle interventions for Hashimoto’s, hypothyroidism, and autoimmune conditions.  She decided to take on lifestyle interventions as a personal mission in an effort to help herself and others with Hashimoto’s. Dr. Wentz is the author of the best-selling patient guide “Hashimoto’s Thyroiditis” Lifestyle Interventions for Finding and Treating the Root Cause”. For future updates, make sure to follow her on Facebook!

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