The Best Digestive Enzyme Supplements & How to Use Them

A Guide to Choosing Digestive Enzymes and Other Gut Health Supports

• Digestive Enzymes|
• Who Needs Them?|
• Choosing Enzymes|
• Microbiome First|
• Other Gut Supplements|
• Summary|

Digestive enzymes help us digest our food, so you might think that if you’re having digestive issues, it must be because you’re lacking those enzymes.

However, an enzyme deficiency is rarely the primary issue in poor digestive health. Sure, there are times when a digestive enzyme supplement may be helpful. But I always suggest that my clients who struggle to digest their food make more fundamental changes to their diet and gut microbiome first.

Let’s look at what digestive enzymes can do, the conditions and symptoms they may help, and when to give them a try.

What Are Digestive Enzymes?

Enzymes are proteins that help make chemical reactions happen in the body. Digestive enzymes are specific types of enzymes that help us digest and extract nutrients from the foods we eat 1.

Different digestive enzymes play specific roles in digestion. The most abundant digestive enzymes include 1: 

• Amylases: Digestive enzymes produced by the salivary glands and pancreas that break down carbohydrates and starches into simpler sugars. This happens in the mouth and small intestine.
• Proteases: Enzymes produced by the stomach, pancreas, and small intestine that digest protein. Examples include trypsin, chymotrypsin, and carboxypeptidase. 
• Lipases: Secreted by the pancreas, lipases break down dietary fats into free fatty acids and glycerol.

Another relevant digestive enzyme is lactase. This enzyme digests the lactose (a type of carb) in milk and is important if you eat dairy 2. It can be useful in supplement form.

Symptoms of Digestive Enzyme Insufficiency

If you don’t have enough digestive enzymes, you might develop digestive issues, nutritional deficiencies, or immune dysfunction 3. Potential symptoms of common digestive enzyme insufficiencies include:

• Bloating 4 5
• Diarrhea 4 5
• Excessive gas 4 5
• Nausea 5
• Abdominal pain 5
• Oily stools 4
• Vomiting 5
• Weight loss 4 6

Who Needs Digestive Enzyme Supplements?

People with a medical condition called exocrine pancreatic insufficiency need digestive enzyme supplements because their pancreas doesn’t make enough amylase, protease, and lipase.

Exocrine pancreatic insufficiency (EPI) is often a side effect of other conditions, including 4:

• Chronic pancreatitis
• Cystic fibrosis
• Gastrointestinal surgery
• Pancreatic cancer

About one in 20 people with irritable bowel syndrome (IBS) may also have EPI 7.

A meta-analysis found that pancreatic enzyme replacement therapy can significantly improve fat and nutrient absorption, gut symptoms, and quality of life for those with EPI 8. 

Beyond EPI, the usefulness of digestive enzymes is less clear. Other conditions that might impair the production of digestive enzymes and could call for an enzyme supplement include 3:

• Physical stress
• An excessive workload
• Disruptions in daily routines
• Lack of physical activity
• An unhealthy diet
• Older age 

There is limited research on digestive enzymes for conditions other than EPI, but digestive enzymes may help with:

• Functional dyspepsia (indigestion): Two randomized controlled trials (RCTs) showed that taking digestive enzyme complexes significantly improved quality of life, reduced pain severity, and enhanced sleep quality in people with dyspepsia. There were no reported side effects 9 10.
• Autism: Gastrointestinal (GI) disorders can be very common in autistic people. One RCT found that a protease supplement may have helped reduce autism severity, repetitive behaviors, and GI symptoms in autistic children 11.
• General wellness: In one study of healthy teens and adults, a digestive enzyme complex may have improved quality of life and sleep, along with iron levels and white blood cell counts 3.
• Plant protein digestion: An RCT showed that adding certain proteases to a pea protein powder may have enhanced people’s ability to digest and absorb these plant-based proteins 12.
• Uncomfortable fullness: Taking lipase before a fatty meal may reduce feelings of fullness, according to one RCT. It didn’t impact bloating, nausea, or stomach activity, though 13. 

How to Choose the Best Digestive Enzyme Supplements

If you have a known condition, like EPI, that requires digestive enzymes, your doctor can prescribe a high-quality product with the enzyme mixture you need. 

But when you are choosing your own digestive enzyme supplement from a store, it’s hard to know what works best. The best digestive enzyme supplement is a high-quality one that works for you and your symptoms.

As a rule-of-thumb guide, a good digestive enzyme supplement will include:

• Lipase, amylase, and protease: These are the three most abundant digestive enzymes, outlined above. You might see protease listed as papain or bromelain.

Other helpful ingredients, depending on your needs, are:

• Betaine HCl: This supplemental source of hydrochloric acid helps improve acidity in the stomach, which can improve the efficiency of protease enzymes and protein breakdown. Some digestive enzymes come with betaine HCl in them. 
• Lactase: If you have lactose intolerance, lactase will work as a standalone supplement without the need for other enzymes. It also makes sense to moderate your intake of dairy products, of course.
• Alpha-galactosidase: This enzyme breaks down the oligosaccharides in legumes that would normally cause bacteria in the bowel to produce gas. Alpha-galactosidase doesn’t naturally occur in the digestive system, but it can be a useful supplement if beans make you very gassy 14.

Follow the instructions on any digestive enzyme products you try and to allow 2–3 weeks for improvements. If there’s no improvement, you probably don’t need the supplement.

Things to Watch For

Studies that investigated the side effects of digestive enzymes reported little or no issues 9 10 11. This suggests there isn’t much risk to taking them. Some people react poorly to digestive enzymes, typically with gut discomfort. Keep an eye out for symptoms and stop the enzymes if you have any.

You also want to make sure the digestive enzyme product is high-quality. The US Food and Drug Administration (FDA) doesn’t certify supplements, so choose digestive enzyme products that show: 

• GMP certification
• Clearly listed allergen information
• Third-party testing 

Products that don’t follow these guidelines may have poor quality and contain something other than what they claim 15.

If you’re taking medications or other supplements, or you are pregnant, please ask a healthcare professional to assess any digestive enzyme supplement you’d like to try 15.

Finally, caregivers of children with cystic fibrosis (CF) should be aware that digestive enzymes can cause fibrosing colonopathy, a rare but dangerous complication. Always work with a doctor before giving CF kids digestive enzymes 15.

Are Gluten Enzymes Helpful?

Unfortunately, there is very little evidence that digestive enzyme supplements can do a good job of breaking down gluten.

In a nutshell, we don’t have good quality data to support the use of glutenases (gluten-degrading enzymes), such as Aspergillus niger Prolyl Endoprotease (AN-PEP), for people with celiac disease 16 or gluten sensitivities 17 18. 

This doesn’t mean you need to avoid glutenase enzymes. But they don’t sufficiently degrade gluten, so you shouldn’t rely on them to make gluten easier to tolerate.

If you have celiac disease, even traces of gluten can cause real harm to your digestive tract, and the only way to protect your health is to avoid gluten completely.

Before Enzymes, Think Microbiome

Without a good balance of gut bacteria, you might experience symptoms that seem like an enzyme insufficiency—like bloating or gas.

This is why at the clinic we always encourage our clients to work on the fundamentals of gut health, specifically microbiome health, before trying digestive enzymes.

The first step to encouraging a healthy microbiome is to eat a nutrient-rich diet. Fiber (from plant foods like whole grains, legumes, fruits, and vegetables) is the main dietary component that helps good bacteria flourish 19. However, certain types of fiber can trigger gut sensitivities, so it’s usually best to transition to a higher-fiber diet slowly.

Diets that respect a fiber-sensitive gut while still supporting the microbiome include a Paleo diet or (in more tricky food intolerance cases) a low-FODMAP diet. For people without significant food sensitivities, a Mediterranean-style, whole-food diet is another great template to follow.

Gut Supplements to Consider Before Enzymes

Digestive enzymes are not the first supplement I think of when it comes to digestive support. 

After my clients with digestive issues implement a whole-food, nutrient-dense diet, I am more likely to recommend probiotics, herbal antimicrobials, glutamine, and prebiotics (in that order). 

These supplements don’t directly digest food, but they support the health of the entire gut ecosystem and often erase any thought of digestive enzymes.

Probiotics

Probiotics can improve leaky gut, reduce inflammation, increase levels of beneficial bacteria, and alleviate dysbiosis 20. They can also fight microbial (bacterial, fungal, or parasitic) infections or overgrowths 21 22 23 and improve IBS 24, IBD 24, and constipation 25.

The probiotic protocol we use in the clinic involves taking these three probiotics together: a blend of Lactobacillus and Bifidobacterium species, a probiotic yeast from the Saccharomyces genus, and a soil-based probiotic. 

Typically, it takes 2–3 months for our clients to see the full benefits of probiotics.

Herbal Antimicrobials 

In the clinic, we often recommend herbal antimicrobials when dietary improvements and probiotics haven’t fully cleared our clients’ symptoms. 

Herbal antimicrobials, such as berberine 26 27, peppermint oil 28, Artemisia absinthium 29, Boswellia serrata 29, and oregano oil 30, can help various gastrointestinal conditions, often with fewer side effects than antibiotics 30.

In a small clinical trial our team conducted, herbal antimicrobials may have eradicated SIBO in about 40% of patients. That’s close to the 50–60% eradication rate of antibiotics 31 32. Even better, when combined with probiotics, herbal antimicrobials may be almost as effective as antibiotics taken with probiotics (86% 21).

Typically, the protocol we recommend looks like this (with or without food):

• Take 3 capsules of Biota Clear 1a twice daily together with Biota Clear 1b.
• Rotate with Biota Clear 2a + Biota Clear 2b after one month.

Glutamine 

For some clients with persistent signs of gut inflammation, we’ll often recommend glutamine. Glutamine may reduce inflammation 33 and leaky gut [34] by supporting the strength of tight junctions in the intestinal wall 35 36. Compared to placebo, glutamine can reduce leaky gut and improve IBS symptoms to a significant degree 34.

Depending on our clients’ needs, we might recommend our Gut Rebuild Nutrients, a mixture of herbs and 1,500 mg of L-glutamine, or pure L-glutamine, each serving of which contains 9,600 mg.

Prebiotics 

Prebiotics can feed and thus increase the levels of beneficial bacteria in the gut 37 38. In the clinic, we’ve found prebiotics can benefit people with Candida overgrowth by feeding gut bacteria that crowd out this fungus. However, per my comments above, prebiotics are types of fiber that may exacerbate a sensitive gut if introduced too soon. They may be useful after gut health has stabilized. 

Most of our clients who are early in the gut healing process can take 3–5 mg of prebiotics per day (a common addition to many probiotics) without symptoms. In clients with more stable gut health (or lingering symptoms suggestive of Candida), we’ll often recommend adding more gradually.

Digestive Enzymes in Context

Digestive enzymes can have their place, but we’ve had mixed results with them in the clinic. Instead, we’ve found several more effective options—like dietary changes and probiotics—for improving overall gut health and supporting good digestion. 

If you still want to try digestive enzymes, choose a reputable product and take it as directed for 2–3 weeks. If a digestive enzyme supplement doesn’t help much in that time frame, you probably don’t need the extra enzymes.

For a more in-depth gut healing protocol, you can try the 8-step process described in Healthy Gut, Healthy You. Or, reach out to our clinic for an appointment and more personalized help with your gut health journey.

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