Probiotics vs. Digestive Enzymes

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Are heartburn, gas, bloating, and constipation ruining your day? Poor gut health can interfere with your quality of life, leaving you tired and in pain. How effectively you break down food, absorb nutrients, and eliminate waste depends on your digestive enzymes and microbiota health.

Diet, infections, age, medications, stress, and sleep can all affect your digestive health. But before you reach for an antacid or laxative, consider adding some digestive enzymes and/or probiotics to your diet. Both benefit digestion, but their roles differ.

So how do you choose which is right for you?

Digestive Enzymes vs. Probiotics


Digestive Enzymes Probiotics
Digestive enzymes are proteins made by the human body that break down food and support digestion. Probiotics are live microorganisms that replenish the good bacteria in the gut to help restore and maintain intestinal health.
Tips for the ideal digestive enzyme supplement:
• Choose a broad-spectrum digestive enzyme supplement providing enzymes that support the digestion of carbohydrates, proteins, and fats, including amylase, protease, and lipase. Additional enzymes such as bromelain, papain, alpha-galactosidase, lactase, and cellulase may be included.

• Choose lactase enzyme-specific products in case of lactose intolerance. 

• The product label should clearly outline the enzyme’s name, source, amount (in milligrams), and active units.

• Always read and follow the label.
Tips for the ideal probiotic supplement:
• Consider which genera, species, and strains best suit your age, health, and lifestyle. Choose products containing multiple probiotic strains to provide better diversity and support overall intestinal health.

• Select products that provide at least 5–100 billion colony-forming units (CFUs). Lower CFU counts are ideal for gut microbiota maintenance, and higher CFU counts can support specific conditions such as antibiotic-associated diarrhea.

• Proper storage instructions are located on the label. Some probiotic supplements must be kept refrigerated, while others are stable without refrigeration. 

• Always read and follow the label.
Digestive enzyme supplements:
• Aid in digestion
• Match natural metabolism
• Support gastrointestinal concerns, such as gas, bloating, and indigestion
• Improve nutrient absorption
• Regulate bowel movements
• Generally taken with a meal
Probiotic supplements:
• Help support gastrointestinal health
• Promote a favourable gut flora
May also help with
• Food allergies/sensitivities
• Mood balance
• Immune support
• Protection against pathogenic bacteria
• Generally taken with a meal
Examples of digestive enzymes:
• Amylase breaks down carbohydrates
• Lipase breaks down lipids or fats 
• Proteases break down proteins
• Lactase breaks down lactose
• Sucrase breaks down sucrose 
Examples of probiotic strains:
• Lactobacillus acidophilus
• Lactobacillus rhamnosus
• Lactobacillus plantarum
• Bifidobacterium longum
• Bifidobacterium bifidum
• Bifidobacterium breve

Digestion Basics

Digestion is an important process that involves breaking down food into substances that can be used by the body. Digestion begins in the mouth, and as we chew, our food is mixed with saliva, which contains digestive enzymes. Once swallowed, food continues through the digestive tract, where it encounters enzymes produced by the pancreas and small intestine.

Digestive Enzymes are Essential

Digestive enzymes are proteins made by the body to help us digest food. Digestive enzymes can also be found in some foods, such as pineapple, papaya, and fermented foods. Different enzymes in the digestive tract perform different tasks.

Here are the main digestive enzymes:

  • Amylase breaks down carbohydrates
  • Lipase breaks down lipids or fats
  • Proteases break down proteins
  • Lactase breaks down lactose
  • Sucrase breaks down sucrose

Digestive Enzyme Deficiency is a Problem

Without enzymes, it would take a very long time to break down food, and the nutrients would not be fully absorbed. A deficiency of digestive enzymes can often occur resulting from: [1][2]

  • Poor eating habits, including eating too fast or too late and not chewing enough
  • Too many refined carbohydrates, fat, animal proteins, and cooked food
  • Increasing age
  • High-stress levels
  • Medications such as proton pump inhibitors and antacids
  • Medical conditions such as pancreatic insufficiency, celiac disease, and dysbiosis

Our bodies may also not produce enough specific enzymes, such as cellulase and lactase. And without proper enzyme function, a lot of digestive problems can result, such as:

  • Food sensitivities
  • Bloating, gas
  • Diarrhea, constipation
  • Nutrient deficiencies
  • Fatigue
  • Weakened immunity
  • Skin irritations

Digestive Enzyme Supplements Can Help!

Digestive enzymes from plants, animals, and bacteria/fungi provide the main enzymes needed to break down food and help: [1]

  • Maintain digestive function
  • Match natural metabolism
  • Support gastrointestinal concerns, such as gas, bloating, or indigestion
  • Improve nutrient absorption
  • Regulate bowel movements

The Ideal Digestive Enzyme Supplement

Getting the best digestive enzyme supplement and using it correctly can significantly affect your digestive health. Although digestive enzymes are generally well-tolerated with minimum side effects, it’s important to consider these key points when choosing and using a digestive enzyme supplement:

  • Choose a broad-spectrum digestive enzyme supplement providing enzymes that support the digestion of carbohydrates, proteins, and fats, including amylase, protease, and lipase. These supplements may include additional enzymes such as bromelain, papain, alpha-galactosidase, lactase, and cellulase.
  • Choose lactase enzyme-specific products in case of lactose intolerance to prevent symptoms of bloating, gas, flatulence, cramping, and diarrhea. 
  • The product label should clearly outline the enzyme’s name, source, amount (in milligrams), and active units.
  • Take a digestive enzyme with meals to help food break down.

The Microbiota and Probiotics are Important

Now that you’re familiar with the role of digestive enzymes, let’s focus on the importance of the microbiota and probiotics. The digestive tract is home to several microorganisms, including good bacteria, that help establish what’s known as the gut microbiota. There are 100 trillion bacterial cells in the intestines – about 10 times more than human cells! [3] Research continues to demonstrate the importance of the microbiota’s role in our health and its important functions, including: [3][4]

  • Supporting healthy digestion
  • Strengthening the gut barrier
  • Producing vitamins
  • Synthesizing neurotransmitters such as serotonin
  • Metabolizing drugs
  • Protecting against different pathogens
  • Regulating immunity

A Disrupted Microbiota is a Problem

Any imbalance in the community of the gut’s microbes can lead to dysbiosis, often triggered by: [5]

  • A diet high in sugar and low in fibre
  • Alcohol use and smoking
  • Antibiotics and other medications
  • Toxin exposure
  • Infections and inflammation
  • Stress
  • Poor hygiene

Dysbiosis can lead to increased inflammation and leaky gut associated with conditions such as irritable bowel syndrome, reflux, food sensitivities, allergies, asthma, and obesity. [6]

Probiotics Can Help!


Healthy digestion probiotics and prebiotics for microbiome intestine.

Probiotics are live microorganisms that replenish the good bacteria in your gut, restoring balance and improving digestion. [7][8] Probiotics have also been shown to:

  • Improve lactose intolerance
  • Support immunity
  • Lower serum cholesterol
  • Relieve traveller’s diarrhea and antibiotic-associated diarrhea
  • Control food allergies/sensitivities
  • Protect against pathogenic bacteria
  • Balance mood

The Ideal Probiotic Supplements

Many beneficial bacteria are found in fermented foods and supplements, often identified by their genus, species, and strain. When choosing the right probiotic formula for your needs, it’s important to:

  • Consider which genera, species, and strains are best suited for your age, health, and lifestyle. The most common general are Lactobacillus and Bifidobacterium. Choose products containing multiple strains to provide better diversity and support small and large intestinal health.
  • Choose probiotic supplements that provide at least 5–100 billion colony-forming units (CFUs). Lower CFU counts are ideal for gut microbiota maintenance. Higher CFU counts can support specific conditions such as antibiotic-associated diarrhea. 
  • Read the label for proper storage instructions. While some probiotic supplements need to be kept refrigerated, others use advanced microencapsulation technology, which keeps the probiotic stable without refrigeration.

Commonly Asked Questions About Digestive Enzymes and Probiotics


1. Can digestive enzymes and probiotics be taken together?

Yes, digestive enzymes and probiotics can be taken together at mealtimes. While digestive enzymes are most often taken with food, some probiotics may be recommended to be taken away from food. Read product labels to ensure you are using products at the appropriate times.

2. When should digestive enzymes and probiotics be taken? 

In general, digestive enzymes should be taken shortly before eating, and probiotics should be taken shortly after eating. Both can be taken with a meal. Always check the product label for proper dosing and timing.

3. Do digestive enzymes kill probiotics?

Digestive enzymes and probiotics perform differently but complement each other. Digestive enzymes do not destroy probiotics, and vice versa.

4. What’s best for bloating, digestive enzymes, or probiotics?

It depends on what’s causing the bloating. If you have trouble digesting certain foods and experience bloating after eating, digestive enzymes may help. If bloating results from an imbalanced microbiota, probiotics may help.

Stephanie Rubino, ND

Stephanie Rubino, ND

A licensed naturopathic doctor with training from the Canadian College of Naturopathic Medicine

References :
  1. Swami O, Shah N. Functional dyspepsia and the role of digestive enzymes supplement in its therapy. Int J Basic Clin Pharmacol. 2017; 6:1035. 
  2. Ianiro G, Pecere S, Giorgio V, et al. Digestive enzyme supplementation in gastrointestinal diseases. Curr Drug Metab. 2016; 17(2):187-93.  
  3. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017; 474(11):1823-36.   
  4. Rowland I, Gibson G, Heinken A, et al. Gut microbiota functions: Metabolism of nutrients and other food components. Eur J Nutr. 2018; 57(1):1-24.  
  5. Hrncir T. Gut microbiota dysbiosis: Triggers, consequences, diagnostic and therapeutic options. Microorganisms. 2022; 10(3):578.  
  6. Carding S, Verbeke K, Vipond DT, et al. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015; 26:26191.  
  7. De Filippis F, Pellegrini N, Vannini L, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2016; 65(11):1812-21.   
  8. Gagliardi A, Totino V, Cacciotti F, et al. Rebuilding the gut microbiota ecosystem. Int J Environ Res Public Health. 2018; 15(8):1679. 
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