Synergies & Differences Between Digestive Enzymes and Probiotics

You are here:

Table of Contents

Digestive enzymes and probiotics are not the same, but they are both essential to healthy digestion. Probiotics support balance in your gut microbiome, while digestive enzymes break down the food we eat.

Inadequate amounts of one or the other can negatively impact your gut health. If you’re not getting enough in your diet, both are available in supplement form whenever your digestive health needs a boost.

Colorado residents: Looking for a healthcare provider to help you get to the root of your gut problems? Set up a free 15-minute consultation to learn more about how we help patients identify and reverse the underlying causes of their issues so they can get back to living.

The Difference Between Digestive Enzymes and Probiotics

Digestive enzymes and probiotics are often confused with one another, but there are some key differences, starting with how both are found in the body. The body doesn’t produce probiotics naturally, but it does produce different types of digestive enzymes.

They also have different impacts on digestive health. 

Probiotics are a more holistic part of gut health, helping you maintain a good balance of healthy gut bacteria. Digestive enzymes have a more direct impact. They help your body break down food and macronutrients into smaller, more absorbable pieces for nutrition.

What Are Digestive Enzymes?

Digestive enzymes are naturally occurring compounds synthesized and secreted by organs like the salivary glands, stomach, pancreas, and small intestine. Together, they help your body break down the food you eat.

There are many different types of digestive enzymes. Where they’re produced along your digestive tract determines the effects they’ll have on the nutrients you consume: 

Digestive EnzymeWhere ProducedTargeted Nutrients
AmylaseSalivary glands, pancreasCarbohydrates
MaltaseSalivary glands, pancreasMaltose and similar sugars
TrypsinSmall intestineProteins
LactaseSmall intestineLactose
SucraseSmall intestineSucrose

When you eat something, your digestive enzymes activate to break down that food into a substance your body can absorb. That includes proteins into amino acids, fats into fatty acids, or carbs into simple sugars.

If your gut health is compromised, this digestive process may be disrupted, and you may not get the nutrition you need for overall health. This can impact everything about how you feel, including energy levels, gut discomfort, and metabolic function.

Additional health benefits of digestive enzymes include:

  • Reduced digestive discomfort. Healthy levels of digestive enzymes reduce symptoms like gas, bloating, indigestion, and abdominal pain. This may be thanks to the enzymes’ effects on more difficult-to-digest foods.
  • Improved symptoms from irritable bowel syndrome (IBS). Research shows that enzyme therapy works particularly well with patients with diarrhea-predominant variety, or IBS-D.
  • Symptom relief from food intolerances like lactose intolerance. People who take lactase supplements before ingesting dairy products (such as Lactaid, the one found in most stores) are less likely to experience the unpleasant side effects of lactose.
  • Enhanced energy levels. Chronic malabsorption of carbohydrates and proteins contributes to fatigue. Efficient, consistent digestion supports your body’s functions, including energy levels.
  • Weight management. Proper digestion and optimized absorption of nutrients may play a part in regulating your appetite. Your digestive health is also a key contributor to a healthy metabolism.
  • Reduced risk of malabsorption. Perhaps most importantly, healthy digestion means your body gets what it needs from your food. Poor digestion puts you at risk for chronic conditions that go well beyond your gut health.

Are digestive enzymes probiotics? Digestive enzymes are not probiotics, but the two do work together to support healthy digestion.

What Are Probiotics?

Probiotics are live microorganisms like bacteria and yeasts that are ingested through certain foods or probiotic supplements. When they’re at healthy levels, they promote a good balance of intestinal microflora and beneficial bacteria. 

In simpler terms, they can help your gut return to healthier function after an influx of unhealthy bacteria. This can be caused by food intolerances, chronic stress, antibiotics, digestive issues, or autoimmune conditions.

Additional benefits of probiotics include:

  • Improved nutrient absorption. Probiotics create a healthier environment for digestive enzymes to do their work. This reduces your risk of malabsorption and inflammatory conditions caused by poor nutrition.
  • Lower risk of chronic gastrointestinal conditions like IBS and inflammatory bowel disease (IBD). A diverse gut microbiome reduces your risk of bacterial infections that contribute to gut-related conditions.
  • Enhanced intestinal barrier function. This can improve symptoms caused by leaky gut syndrome or intestinal permeability. Leaky gut can cause chronic gut problems and worsen symptoms of IBS. 
  • Bowel movement regularity. Patients with loose stools, constipation, or inconsistent bowel movements often find relief after starting probiotics supplementation. This may be thanks to the probiotics’ effects on the gut microbiome.
  • Improved immune system function. A healthy gut is important to immune system health. It strengthens your body’s responses against infections and reduces inflammation, two critical factors in preventing disease. 
  • Protection against infection, including urinary tract infections (UTIs). Probiotics, especially Lactobacilli, are essential to a healthy urogenital tract (the organs of the urinary and reproductive systems).
  • Enhanced skin barriers. Both oral and topical probiotics can have a positive effect on acne-causing bacteria and skin conditions like psoriasis, eczema, and allergic inflammation.
  • Lower risk of gum disease. A healthy oral microbiome is important in preventing oral infections, as buildups of harmful bacteria can contribute to gum inflammation and periodontal disease.

How Digestive Enzymes and Probiotics Work Together

Digestive enzymes and proteins work together to support your digestive health. Enzymes break food into absorbable nutrients, while probiotics create a more conducive environment for ideal absorption. They help digestive enzymes work more efficiently.

This enhanced digestion isn’t just good for your gut health; it’s important to your overall well-being. Any disruption can lead to uncomfortable digestive symptoms, a weakened immune system, and a higher risk of chronic health conditions.

Foods with Digestive Enzymes

Unlike probiotics, digestive enzymes naturally occur in the body. Some people don’t have enough of them due to health conditions causing enzyme insufficiency. Others have a deficiency in certain types of enzymes that can cause food intolerances, gut discomfort, or malabsorption. 

Much like a detox, eating foods that are sources of digestive enzymes is an excellent natural remedy for improved digestion. Foods rich in digestive enzymes include:

  • Papaya (for the enzyme papain)
  • Pineapple
  • Mango
  • Avocado
  • Bananas
  • Kefir
  • Sauerkraut
  • Kiwi
  • Honey
  • Ginger

Note: If you have a condition that causes digestive enzyme insufficiency, an enzyme supplement may be the best way to ensure you get the nutrition you need.

Visit the PrimeHealth store for medical grade, third-party tested, evidence-based supplements to support your gut health and overall wellness.

Foods with Probiotics

Your body has trillions of microbes within its microbiome, but probiotics themselves aren’t naturally-occuring. They’re passed through the nutrition we eat or drink from birth.

Prebiotics, the “food” for microflora, are also consumed through food and supplements. These are typically found in high-fiber plants and work together with probiotics to support a healthy digestive system.

You can boost your probiotic profile by consuming more fermented, probiotic-rich foods. These include:

  • Yogurt
  • Kefir
  • Sauerkraut
  • Kimchi
  • Miso
  • Buttermilk
  • Tempeh
  • Kombucha
  • Cottage cheese
  • Pickles

Should You Take Digestive Enzyme or Probiotic Supplements?

You may benefit from taking probiotics if your gut health is out of balance, you have a dysbiotic gut microbiome, or you experience frequent gastrointestinal symptoms like bloating, acid reflux, or IBS. These supplements can increase the good bacteria in your gut and crowd out the pathogenic (disease-causing) bacteria.

Probiotics are also helpful after a round of antibiotics, as these deplete your microbiome of valuable bacteria.

There are different kinds of probiotic supplements available for various purposes, but the most common come from two main species: Bifidobacteria and Lactobacillus. They can be taken separately, but when combined, they are frequently used to treat inflammatory bowel diseases. 

You may benefit from taking digestive enzymes if your body struggles with enzyme production (like if you have an enzyme deficiency) or nutrient absorption. 

Side effects of digestive enzyme insufficiency include:

  • Stomach pain or cramps
  • Diarrhea
  • Bloating or gas
  • Unexplained weight loss
  • Changes to bowel movements, especially oily stools

Common causes of digestive enzyme insufficiency are:

  • Congenital sucrase-isomaltase deficiency: This rare genetic disorder affects the body’s ability to digest sugars like sucrose or maltose. It’s typically identified in young children after they start consuming sugars and starches.
  • Exocrine pancreatic insufficiency (EPI): This occurs when your pancreas doesn’t produce enough enzymes needed to digest food in the small intestine. People with conditions like diabetes, cystic fibrosis, pancreatic cancer, celiac disease, and IBD are at a higher risk.
  • Lactose intolerance: This is when your body doesn’t produce enough lactase to break down lactose, the sugar found in dairy products. This is one of the most common food sensitivities linked to digestive enzymes.

Talk to your healthcare provider if you think you may have a condition at the root of your digestive issues. Symptoms can mimic those of digestive conditions like IBS.

Subscribe to our newsletter to stay informed on Health Topics like this!
Get primehealth updates right to your inbox

Can You Take Digestive Enzymes and Probiotics Together?

You can take digestive enzymes and probiotics together. Both are important to digestive and overall gut health. Whether you need one more than the other depends on your symptoms, existing nutritional deficits, and current health conditions.

It’s always best to talk to your primary care doctor before starting a regimen of supplements. There may be other causes at the root of your digestive health concerns.


What is digestive enzyme insufficiency?

Digestive enzyme insufficiency is when the body cannot produce adequate amounts of enzymes for efficient digestion. This can result in uncomfortable symptoms like bloating and diarrhea or nutrient malabsorption.

Is it better to take probiotics or digestive enzymes?

There is no correct answer as to whether it’s better to take probiotics or digestive enzymes; it all depends on your symptoms and existing health conditions. Some supplements include both for optimal digestive health.

Is it OK to take digestive enzymes every day?

It is OK to take digestive enzymes every day, but you may not need to as the causes of your insufficiency or symptoms are addressed. People with chronic conditions or known food intolerances to gluten, lactose, or other food products may benefit from a daily supplement, especially when eating an offending food.


  1. Rothman, S., Liebow, C., & Isenman, L. (2002). Conservation of digestive enzymes. Physiological Reviews, 82(1), 1-18. 
  2. Ullah, H., Di Minno, A., Piccinocchi, R., et al. (2023). Efficacy of digestive enzyme supplementation in functional dyspepsia: A monocentric, randomized, double-blind, placebo-controlled, clinical trial. Biomedecine & Pharmacotherapy, 169, 115858. 
  3. Graham, D.Y., Ketwaroo, G.A., Money, M.E., et al. (2018). Enzyme therapy for functional bowel disease-like post-prandial distress. Journal of Digestive Diseases, 19(11), 650-656. 
  4. Zhou, Y., Jiang, Z., Lv, D., et al. (2009). Improved energy-utilizing efficiency by enzyme preparation supplement in broiler diets with different metabolizable energy levels. Poultry Science, 88(2), 316-322.
  5. Tucci, S.A., Boyland, E.J., & Halford, J.C. (2010). The role of lipid and carbohydrate digestive enzyme inhibitors in the management of obesity: a review of current and emerging therapeutic agents. Diabetes, Metabolic Syndrome, & Obesity, 10(3), 125-143. 
  6. Roxas, M. (2008). The role of enzyme supplementation in digestive disorders. Alternative Medicine Review, 13(4), 307-314. 
  7. Catanzaro, R., Sciuto, M., & Marotta, F. (2021). Lactose intolerance: an update on its pathogenesis, diagnosis, and treatment. Nutrition Research, 89, 23-34. 
  8. Zhang, H., Duan, Y., Cai, F., et al. (2022). Next-generation probiotics: Microflora intervention to human diseases. Biomed Research International, 5633403. 
  9. Judkins, T.C., Archer, D.L., Kramer, D.C., et al. (2020). Probiotics, nutrition, and the small intestine. Current Gastroenterology Reports, 22(1), 2. 
  10. Parker, E.A., Roy, T., D’Adamo, C.R., et al. (2018). Probiotics and gastrointestinal conditions: An overview of evidence from the cochrane collaboration. Nutrition, 45, 125-134.
  11. Aleman, R.S., Moncada, M., & Aryana, K.J. (2023). Leaky Gut and the ingredients that help treat it: A review. Molecules, 28(2), 619. 
  12. Wang, F., Zhao, T., Wang, W., et al. (2022). Meta-analysis of the efficacy of probiotics to treat diarrhea. Medicine, 101(38), e30880. 
  13. Mazziotta, C., Tognon, M., Martini, F., et al. (2023). Probiotics mechanism of action on immune cells and beneficial effects on human health. Cells, 12(1), 184. 
  14. Falagas, M.E., Betsi, G.I., Tokas, T., et al. (2006). Probiotics for prevention of recurrent urinary tract infections in women: a review of the evidence from microbiological and clinical studies. Drugs, 66(9), 1253-1261.
  15. He, Y., Zhu, L., Chen, J., et al. (2022). Efficacy of probiotic compounds in relieving constipation and their colonization in gut microbiota. Molecules, 27(3), 666. 
  16. Gao, T., Wang, X., Li, Y., et al. (2023). The role of probiotics in skin health and related gut-skin axis: a review. Nutrients, 15(14), 3123. 
  17. Roudsari, M.R., Karimi, R., Sohrabvandi, S., et al. (2015). Health effects of probiotics on the skin. Critical Reviews in Food Science and Nutrition, 55(9), 1219-1240. 
  18. Inchingolo, F., Inchingolo, A.M., Malcangi, G., et al. (20230). The benefits of probiotics on oral health: systematic review of the literature. Pharmaceuticals, 16(9), 1313. 
  19. Ianiro, G., Pecere, S., Giorgio, V., et al. (2016). Digestive enzyme supplementation in gastrointestinal diseases. Current Drug Metabolism, 17(2), 187-193. 
  20. Syngai, G.G., Gopi, R., Bharali, R., et al. (2016). Probiotics – the versatile functional food ingredients. Journal of Food Science & Technology, 53(2), 921-933. 
  21. Abdelhamid, A.G., El-Masry, S.S., & El-Dougdoug, N.K. (2019). Probiotic lactobacillus and bifidobacterium strains possess safety characteristics, antiviral activities and host adherence factors revealed by genome mining. EPMA Journal, 10(4), 337-350. 
  22. Alkaade, S. & Vareedayah, A.A. (2017). A primer on exocrine pancreatic insufficiency, fat malabsorption, and fatty acid abnormalities. American Journal of Managed Care. 23(12 Suppl), S203-S209. 
PrimeHealth Newsletter
Get tips & advice right to your inbox, plus stay up to date on PrimeHealth group visits and services.

Share this Post