(Woodpath is an education site focused exclusively on gut health. Our articles are researched by clinical nutritionists and contain citations at the end of the page.)

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.

The bottom of this page contains product recommendations. First, let's learn the science behind both.

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.

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.

Luckily, you can get the enzymes you need in certain foods. These foods — some of which are listed below — can aid the digestive system in getting back on the right track.

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. It's important to research which enzymes are best suited to tackle the specific digestive issue at hand.


Probiotics are live, beneficial bacteria found throughout the gut and digestive tract. They keep bad bacteria at bay and promote a healthy digestive system. Probiotics are not naturally produced by the body but are introduced when you 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, 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. There are several strains of probiotics. Each provide differing benefits. Two of the most popular are:


  • Aids in food breakdown
  • Helps the body absorb nutrients
  • Kills bad bacteria and organisms
  • Prevents UTI


  • Treats several conditions such as irritable bowel syndrome, infection from H. pylori, and necrotizing enterocolitis
  • May boost immunity
  • Helps alleviate symptoms of eczema in children

Keep in mind that probiotics are as sensitive as digestive enzymes. The bacteria in probiotic supplements are living organisms and cannot tolerate heat or light. They must remain in the refrigerator. Higher temperatures and direct sunlight will kill off the bacteria.

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 distresses.
  • 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).

Product Recommendations

Use the guide above — along with doctor supervision — to determine which supplement is right for you. Then, we recommend choosing from the following:


Digestive Enzymes

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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
  • 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 Reviews2017; 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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