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The Digestion Connection: Digestive Enzymes, Malabsorption & Hashimoto's

I've had digestive issues for as long as I can remember, and for me, they were one of the most noticeable and frustrating symptoms that I had. In fact, if I hadn't of had them, I often wonder if I would even have my diagnosis now, because it was the one issue that I couldn't put up with and drove me to keep digging into what was going on.


Symptoms of hypothyroidism usually first show up in children as constipation, because reduced thyroid hormone affects the motility (movement) of the gut. Over the years I have found that the majority of my clients with Hashimoto's or any autoimmune condition for that matter, have some form of digestive issue and many don't connect it to their condition. The research suggests there's actually a gut - thyroid axis, meaning it has a direct impact on thyroid function. I frequently see people who have just accepted the daily struggle of their nagging symptoms as simply being “the way their system is", as I almost did too. Some no longer even report these symptoms to their doctor because they have simply started to view them as normal.


However, symptoms such as recurring constipation, diarrhoea, stomach pain, having undigested food in your stool, gas and bloating after eating, are not symptoms you need to live with. For many people, these issues can be resolved fairly rapidly by taking digestive aids such as digestive enzymes, stomach acid and bile support. In fact over 80% of my clients report feeling better with digestive support supplements.


Digestive challenges can range from not digesting your protein properly (preventing you from extracting iron and B12 from your food), to struggles with breaking down starches and fats, food intolerances, leaky gut and overgrowths such as SIBO, which causes inflammation and malabsorption of nutrients in the small intestine.


Many patients with thyroid issues have gallbladder issues leading to problems digesting and absorbing fat, which can result in a depletion of important nutrients that are no longer being well absorbed, including fat-soluble vitamins A, D, E and K, as well as essential fatty acids. The reason is because the gall bladder needs thyroid hormones in order to help it retract and function properly. Without them, a bile sludge builds up and causes gall stones.


A deficiency in pancreatic enzymes can also be at the root cause of fat malabsorption issues. While you've probably heard of the pancreas (where these key fat digestion enzymes are produced), you may not be aware of how important the pancreas is, and how supplementing with pancreatic enzymes can make all the difference in uncomfortable and embarrassing digestive symptoms.


The pancreas consists of two tightly connected glands, each with a distinct function. One gland (referred to as the “exocrine” pancreas) focuses on producing enzymes to help with the digestion of food and the other gland, referred to as the “endocrine” pancreas, produces hormones such as insulin and glucagon.

Insulin and glucagon are released directly into the bloodstream, whereas pancreatic enzymes are released via a duct into the small intestine. Pancreatic hormones help control how the body uses and stores glucose. Abnormal levels of thyroid hormone are associated with blood sugar abnormalities (and poor insulin control), and abnormal levels of pancreatic hormones have been linked to metabolic disorders, such as diabetes. Interestingly blood sugar imbalances can drive inflammation and increase thyroid antibodies, causing a vicious cycle if not addressed.


But how do pancreatic enzymes support fat digestion and the healthy absorption of nutrients? And why does this often go wrong in those with Hashimoto’s?

Our pancreas works, along with our liver and gallbladder, to digest and absorb fats. If we’ve eaten a fatty meal, bile (a substance produced by the liver and stored in the gallbladder) is released from the gallbladder into a duct leading to the small intestine. The role of bile is to break down fats into tiny globules that can be more easily dissolved. At the same time, the pancreas releases its own pancreatic enzymes and pancreatic juice, mixing with the bile and tiny globules of fat. These secretions work together to emulsify and dissolve fats in the small intestine. Pancreatic juices also help with digesting protein and carbohydrates, as well as neutralising all of the digested food, which is initially very acidic, in order to fend off bacteria. All of these actions allow nutrients to be more readily extracted and absorbed (plus, it ensures that we don’t experience unpleasant stomach and bowel symptoms).

Without adequate bile and pancreatic enzymes, many essential nutrients can be lost and excreted with other wastes in the stool, leading to nutrient deficiencies including fatty-acid deficiencies. Additionally, our foods will not be fully digested and may linger for too long in the digestive tract. This can result in us developing food sensitivities or small intestinal bacterial overgrowth (SIBO) for example.

A key marker I look at is Pancreatic Elastase. Levels can be tested via a stool test at your GP or as part of a comprehensive functional gut health analysis (also a stool test).


Low levels of pancreatic elastase can be associated with:

  • Gallstones

  • Hypochlorhydria (low stomach acid), especially if H. pylori is present

  • SIBO

  • Heavy metal toxicity

  • Alcohol use

  • Stress (adrenal insufficiency)

  • Coeliac disease

  • A vegetarian/vegan diet

  • Giardia (and potentially other parasitic) infections

  • Mold toxicity

  • Estrogen dominance

Pregnant women may be at risk for developing low levels of pancreatic elastase, potentially due to gallbladder issues that result from high estrogen. Interestingly, if you look at this list, there are several known triggers for Hashimoto’s, including low stomach acid, SIBO, H. pylori, heavy metal toxicity, coeliac disease (gluten sensitivity), and stress.


Given that about three-quarters of people with Hashimoto’s may have deficiencies in bile and/or pancreatic enzymes (leading to issues with fat absorption), and many also have low levels of stomach acid (leading to difficulties digesting and absorbing nutrients from the protein we eat), it is no wonder that nutrient depletions are so common in people with Hashimoto’s.


If you have a pancreatic enzyme deficiency, you will not be properly digesting and absorbing fats. You may experience digestive symptoms as well as seemingly unrelated symptoms, such as low energy and increased cravings for carbs.


Below are some of the symptoms associated withn enzyme deficiency. If you're experiencing one or more then it could be worth investigating and getting your levels tested.

  • Indigestion/fullness 2-4 hours after a meal

  • Bloating or flatulence 2-4 hours after a meal

  • Undigested food in stool

  • Greasy/floating/light coloured stools

  • Belching

  • Diarrhoea, or oil/grease present during bowel movements

  • Gallbladder pain (right side, under ribs), gallstones, or gallbladder removal

  • Low vitamin levels (A, D, E, and K) – even after supplementing (I see this very often, as the body is not able to absorb and utilise the vitamins in such supplements)

  • Muscle wasting

  • Low energy, increased carb cravings

  • Dry skin

  • Hormonal imbalances (including estrogen dominance) and adrenal issues


These symptoms may indicate a fatty acid deficiency due to fat malabsorption:

  • Soft, cracked, or brittle nails

  • Dry hair, dandruff, or oily scalp

  • Dry, itchy, scaly, or flaky skin, rashes, or eczema

  • Hard earwax

  • Chicken skin (tiny bumps on the back of arms)

  • Joint aches or stiffness

  • Depression

  • Weight loss


Then check if you have any potential fat-soluable vitamin deficiencies:


Vitamin A deficiency:

  • Dry skin

  • Acne and skin disorders

  • Dry eyes

  • Night blindness

  • Poor wound healing

Vitamin D deficiency:

  • Immune system imbalance (getting sick more often)

  • Poor wound healing

  • Fragile bones, bone loss, or pain [23]

  • Muscle weakness

  • Fatigue

  • Depression

  • Hair loss

Vitamin E deficiency:

  • Muscle weakness

  • Numbness and tingling (peripheral neuropathy)

  • Vision problems

  • Coordination and walking difficulties

  • Immune system imbalance

Vitamin K deficiency:

  • Bleeding nose or gums

  • Easy bruising

  • Blood in the urine and/or stool

  • Heavy menstrual periods

  • Excessive bleeding from a cut or wound

Don't forget that these symptoms could be due to a pancreatic enzyme deficiency, gall bladder issues or even SIBO, H.pylori, or low stomach acid. It could even all of these. I've personally found myself to have all of them except a gall bladder issue because they can all be so tightly connected. Don't navigate this alone, because it can get overwhelming and you may not get the best results until all aspects and systems have been reviewed and supported.


If you'd like to book a free call to discuss this further you can do that here.

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