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Two of the most widely used products for digestive and immune health are digestive enzymes and probiotics. Each works in different ways and targets different systems within the body.

Knowing the difference between digestive enzymes and probiotics will help you choose the right supplements for you. Below we talk about the science behind digestive enzymes and probiotics — as well as provide specific product recommendations.

Digestive Enzymes

Digestive enzymes are complex proteins which aid in digestion. They are formed naturally in areas such as the stomach and mouth. However, a majority of enzymes are found within the pancreas. They flow from the pancreas into the small intestines. (Whitcomb & Lowe 2007)

Digestive enzymes include:

  • Lipase — breaks down fats in the gut
  • Amylase — converts starches into sugar
  • Proteases and Peptidases — break down proteins into amino acids

These enzymes work best at a specific temperature and pH level — impacted by your diet. The wrong diet can throw your body out of balance, causing either a highly alkaline or acidic environment.

A body with a high alkaline or acidic environment can disrupt digestive enzymes' ability to function as they should. For example, pepsin — the protease enzyme that helps digest protein in the stomach — works best in the highly acidic (low pH) environment of the stomach.

If stomach acid levels are insufficient, which can occur due to old age, hypothyroidism or nutrient deficiencies, then this enzyme will not be able to perform its duties.

In some cases, the body cannot produce enough enzymes. This can slow digestion — leading to food intolerances. For example, a lack of lactase creates lactose intolerance. Without the help of specific enzymes to break down food, you may experience extreme discomfort from indigestion, gas, and bloating.

Your immune system can also become compromised if you suffer from an enzyme deficiency. A deficiency can prevent the absorption of vital nutrients from the food you eat. This can cause your immune system to shut down — not to mention lead to a slew of other health issues.

Fortunately, you can get the enzymes you need in certain foods.

Food Containing Digestive Enzymes

  • Kefir — contains lipases, proteases, and lactases
  • Papayas and pineapples — contain proteases
  • Mangos — contain amylases
  • Avocados — contain lipases
  • Raw honey — contains diastases, amylases, invertases, and proteases
  • Fermented vegetables such as sauerkraut, kimchi, and miso — contain lactases, lipases, proteases, and amylases

Digestive enzyme supplements are also available and are convenient for those always on the go. They are also more suitable than using food as an enzyme source if the poor enzyme levels are severe or chronic. It's important to research which enzymes are best suited to tackle the specific digestive issue at hand.

Digestive Enzyme Recommendations

If you and your healthcare practitioner decide that enzyme supplements are right for you, we recommend:

Digestive enzymes should be taken with meals.


Probiotics are defined as “live microorganisms which when administered in adequate amounts confer a health benefit on the host." (FAO/WHO, 2001)

They help to keep pathogenic bacteria at bay and promote a healthy digestive and immune system. Probiotics are not naturally produced by the body but are introduced when you take supplements or eat certain foods, including:

  • Apple cider vinegar
  • Kombucha
  • Greek yogurt
  • Fermented vegetables

Healthy gut bacteria can promote a healthy brain and body. The body begins to develop gut bacteria immediately after birth and continues to build throughout its lifespan (Milani, Duranti, Bottacini, Casey, Turroni, Mahony et al., 2017)

However, pesticides in conventional foods, antibiotics, consuming excess sugar, alcohol, and chronic stress can kill off good bacteria within the gut and throughout the rest of the body.

When gut health is not in balance — known as dysbiosis — you may experience symptoms such as indigestion, upset stomach, bad skin, weight changes, autoimmune conditions, inflammation, and constant fatigue.

More and more evidence has indicated that bad gut health is a contributing factor to pro-inflammatory immune responses and also elicits immunosuppressive responses. (Lin & Zhang 2017)

Probiotic Strains

You should consider consuming probiotics that contribute to gut homeostasis or eubiosis.

There are several types of probiotics and benefits are strain specific, so the benefits listed below cover different species and strains within each overall genus.


  • Transformation of dietary polyphenols for use in the body (anti-inflammatory and antioxidant effects)
  • Produce antimicrobial substances to prevent pathogenic bacteria causing harm
  • Prevents UTI
  • Creation of short chain fatty acids which have many health benefits
  • Reduced risk of antibiotic associated diarrhea and infectious diarrhea


  • Promotes healing of the gastrointestinal tract
  • Immune stimulation and modulation
  • Improves gut permeability (leaky gut)
  • Some strains can produce GABA
  • Decreases serum endotoxin levels
  • Reduces severity of infant eczema

Keep in mind that probiotics are as sensitive as digestive enzymes. The bacteria in probiotic supplements are living organisms and usually cannot tolerate excessive heat or light. Some strains must remain in the refrigerator.

Probiotic Recommendations

If you and your healthcare practitioner decide probiotics are right for you, we recommend:

Which Should You Choose?

Choosing the right supplement will help in symptom relief and overall better digestive health.

  • Digestive enzyme supplementation may be beneficial for those with food intolerances, reflux, or other digestive symptoms.
  • Probiotic supplementation may be beneficial for those who suffer from an overgrowth of candida in the body, have a leaky gut, or have recently been on antibiotics.

When to Take Them

  • It doesn't matter what time of day you ingest digestive enzymes — as long as it is within 30 minutes of a meal. This will help with digestion and prevent upset stomach and reflux.
  • Probiotics should ideally be taken in the afternoon after the body has had time to warm up and has been given adequate water and food. Mornings are not an optimal time due to the lack of body warmth and the higher acidity in the stomach (from not eating throughout the night).

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Research Citations

  • Whitcomb D.C., Lowe M.E. Human Pancreatic Digestive Enzymes. Digestive Diseases and Sciences. 2007;52:(1):1-17. doi:10.1007/s10620-006-9589-z
  • FAO/WHO. Health and Nutritional Properties of Probiotics in Food including Powder Milk with Live Lactic Acid Bacteria, 2001.
  • Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado P.S., Arboleya M.S., Mancabelli L, Lugli G. A., Rodriguez J. M., Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, and Ventura, M.  The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiology and Molecular Biology Reviews 2017; 81(4):e00036-17. doi:10.1128/MMBR.00036-17
  • Lin L & Zhang J. Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunology. 2017;18(1):2. doi:10.1186/s12865-016-0187-3
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