Probiotics vs Digestive Enzymes: Which is Better?

Digestive Enzymes Vs. Probiotics: Know The Differences

Digestive Enzymes Vs. Probiotics

Both digestive enzymes and probiotic supplements are promoted for digestive health. Which one is the best to alleviate your symptoms, or should you take both? What is the difference?

While both could alleviate gastrointestinal symptoms like abdominal cramps, bloating, and gas, this is where the similarities end. Digestive enzymes are naturally released in the digestive tract to break down the food you eat.

Probiotic supplements consist of live microorganisms and are intended to supplement the beneficial bacteria which naturally occur in your intestines.

Your particular problem and what your body needs determine whether either digestive enzymes or probiotic supplements could relieve your symptoms.

This article summarizes the advantages and disadvantages of each. We then discuss these points in more detail to help you decide which might help you.

Digestive Enzymes Vs. Probiotics At a Glance

Supplement Bottles

Advantages Of Digestive Enzyme Supplements:

  • Specific supplemental enzymes are supported by research for use as medication when someone has a diagnosed deficiency of a particular digestive enzyme
  • Could support health by increasing the absorption of certain nutrients in the gastrointestinal tract, especially in older persons
  • Could alleviate gastrointestinal symptoms caused by a deficiency of a particular enzyme

Disadvantages Of Digestive Enzyme Supplements:

  • They are only indicated if the body is not naturally producing enough of one or more digestive enzymes
  • They could have side-effects
  • Some enzymes sold as supplements could be broken down by stomach acid before they reach the small intestine
  • Over-the-counter digestive enzyme supplements are not regulated by the FDA so their quality, effectiveness, and safety are not guaranteed

Advantages Of Probiotics:

  • Could relieve gastrointestinal symptoms
  • Could contribute to a healthy gut microbiome and so also to improved general health status
  • Shown to be effective when there is an overgrowth of bad bacteria and fungi in the gut, for example, after a course of antibiotics or severe illness

Disadvantages Of Probiotics:

  • More research is needed to determine which microorganisms have the most benefit for specific conditions
  • They could have side effects
  • Probiotic supplements are not regulated by the FDA, so their quality, effectiveness, and safety are not guaranteed

Editor’s Pick:

Probiotic supplements are more likely to provide an overall health benefit, whereas digestive enzyme supplements are mostly indicated only when there is a clear deficiency of a specific enzyme.

Read on to find out why this is our answer to the question of which would be the best to try out for the relief of gastrointestinal symptoms.

Digestive Enzyme Supplements

Person Holding Supplements

  • What Are Digestive Enzymes

The body naturally produces and releases digestive enzymes in the upper part of the gastrointestinal tract. These complex proteins break down the food you eat into other chemical components so that your body can absorb and use the nutrients.

When specific foodstuffs are not broken down and absorbed, it could cause gastrointestinal and other symptoms. It usually also affects the balance of the gut microbiome.

While there are a variety of different digestive enzymes, the main ones are manufactured and released by the pancreas.

They are:

  • Amylase – made in both the mouth and the pancreas, it breaks down complex carbohydrates into simple sugars.
  • Protease – a pancreatic enzyme that turns protein into amino acids
  • Lipase – a pancreatic enzyme that breaks down fats into fatty acids.

Some other digestive enzymes are lactase which breaks down lactose, the sugar in milk, and sucrase, which changes sucrose, the sugar found in fruits and vegetables. This includes normal table sugar made from sugar cane or sugar beets.

  • What Causes Digestive Enzyme Deficiencies?

A deficiency of one or more specific digestive enzymes could be the result of the body either not producing enough or not releasing the enzyme effectively.

This could be genetically determined, as is often the case in lactose intolerance. It could also be caused by health conditions, in particular disorders of the pancreas like infections, surgery, or cancers.

It also appears that the production of digestive enzymes might naturally slow down with aging, as with other systems in the body.

  • Common Symptoms Of Digestive Enzyme Deficiency

  • Malnutrition, because the body is unable to absorb enough essential nutrients from the small intestine.
  • Unexplained weight loss
  • Abdominal pain and cramping
  • Bloating
  • Gas
  • Diarrhea
  • Oily stools
  • Digestive Enzymes as Medications

The only FDA-approved digestive enzymes are specific pancreatic enzyme products (PEP) to treat people with disorders of the pancreas. They contain a combination of amylase, lipase, and protease. All PEPs have to be approved by the FDA, and they have an enteric coating that prevents the enzymes from being broken down by stomach acid. (1)

There are two other digestive enzyme supplements that are well supported by research and often prescribed by health care professionals, although they are not controlled by the FDA and are available over the counter. The first is those containing lactase for treating lactose intolerance (for example, Lactaid).

The second is a supplement containing alpha-galactosidase (for example, Beano), an enzyme not produced in the body. This enzyme helps to digest the sugar in beans and cruciferous vegetables like cabbage, cauliflower, and broccoli. It might help those who experience bloating and gas after eating these vegetables.

  • OTC Digestive Enzyme Supplements

The general view is that digestive enzyme supplements are only necessary when a person has an actual enzyme deficiency. This can usually be determined by laboratory testing.

There are, however, now numerous over-the-counter digestive enzyme supplements on the market with either one or a combination of enzymes. Manufacturers claim that they promote health by improving digestion, increasing nutrient absorption, and relieving gastric discomfort.

So far, there is not enough scientific evidence to support these claims or the correct dosage and safety of these products. Furthermore, the enzymes could be broken down by stomach acid if the tablets are not enteric-coated.

However, research is ongoing, and a few studies have shown that these supplements could provide relief for various health problems.

One randomized pilot study, for example, found that pancrelipase improved IBS symptoms in the experimental group. The study was, however, very small, with only 49 participants, and only included persons who had IBS characterized by diarrhea. (2)

Currently, many of the promising studies that show that digestive enzymes might benefit gut health, in general, have been animal studies. One such study found that supplementing with pancreatic enzymes improved the composition of the gut microbiome in mice, thereby improving their general nutritional state. (3)

  • Side Effects Of Digestive Enzyme Supplements

Possible side effects of digestive enzyme supplements include:

  • Stomach pain
  • Constipation or diarrhea
  • Nausea
  • Allergic reactions
  • Interactions with other medications

Probiotic Supplements

Probiotic Supplements

What Are Probiotics?

The internationally accepted definition of probiotics is “live microorganisms which, when administered in adequate amounts, confer a health benefit to the host.” (5)

We have in the region of 100 trillion good and bad bacteria living mostly in our large intestines. This colony is referred to as the gut microbiome or microbiota. (4)
Although research is far from finding all the answers, we know that a balanced gut microbiome is essential for overall physical and mental health. Disruption is associated with allergies, poor digestive health, inflammation, autoimmune disorders, and even mental health issues.

If, for whatever reason, the gut microbiome is out of balance, it can be corrected over time through a well-balanced diet and other lifestyle factors. This process could take up to six months. Probiotic supplements can help to restore the microbiome more rapidly.

  • Symptoms Of An Unbalanced Gut Microbiome

When the bad bacteria or fungi in the gut take over, symptoms could include:

  • Bloating and Gas
  • Diarrhea or constipation
  • Skin problems
  • Changes in mood, like being irritable or anxious

These are the obvious symptoms that might occur after, for example, a course of antibiotics. However, because of the extensive role of the gut microbiome in maintaining a healthy body, a long-term imbalance could contribute to various health issues.

Gut microbiome disruption is associated with, not only poor digestive health, but also allergies, inflammation, reduced immunity, autoimmune disorders like IBS, as even mental health issues.

  • Role Of Probiotic Supplements

The live bacteria in probiotics help to restore the balance of the natural gut bacteria.

Interestingly it appears as though the bacteria in these supplements do not colonize the microbiome and only work for a week or two after they are discontinued.

However, they do stimulate an overall shift in the diversity of bacteria in the gut by secreting substances that are beneficial to the digestive tract and the body as a whole. They also help to suppress the overgrowth of bad bacteria and fungi.

There is evidence that probiotics do improve certain conditions, including diarrhea from antibiotics, constipation, irritable bowel disease, colitis and yeast infections. Currently, a lot of research is being done on their possible role in treating other medical conditions.

However, it has become clear that the effect of probiotics varies between people and is also dependent on the specific strain of bacteria in the supplement, as different strains appear to have different health benefits.

A considerable amount of current research is now focused on a better understanding of the microbiome and which imbalances might be associated with different health problems. In the future, this could lead to tailor-made probiotics to target specific medical conditions. (6)

You can learn more about probiotics in our Ultimate Guide to Probiotics.

  • Side Effects Of Probiotic Supplements

Probiotics are generally safe for most people. Potential side effects include:

  • Mild digestive symptoms, like diarrhea, gas, and bloating, especially during the first few days of taking them
  • Allergic reactions that could include allergic rhinitis, commonly known as hay fever
  • More severe side effects in persons with a weakened immune system
  • Risk of infection for persons with a weakened immune system or after a recent serious illness or surgery.


It is clear that both digestive enzymes and probiotic supplements could help to improve your gastrointestinal symptoms. Also that there is not much difference between the symptoms, which either the one or the other might relieve. But this is where the similarities end.

In the end, it is not a matter of whether to choose digestive enzyme supplements or probiotics to relieve gut health issues – it depends on the cause of your problem. Generally, probiotics could benefit everybody, while digestive enzymes might make a big difference if you have a deficiency of a specific enzyme.

You could try out a course of either to see if it helps. However, if you have serious health problems or are currently taking prescribed treatment, you should consult your health care provider before taking even over-the-counter supplements.

Written by Frieda Paton

Frieda is a registered nurse and published author with extensive experience throughout her career in research, scientific writing and journalism. She has now turned to writing full time to share her passion for health and wellness, helping readers to prevent and manage chronic conditions. Frieda lives and works in the small museum town of Pilgrim’s Rest in South Africa.


1.FDA. 2012. Updated questions and answers for healthcare professionals and the public: Use and approved pancreatic enzyme product. FDA.
2. Money, M.E. 2011. Pilot study: a randomised, double blind, placebo controlled trial of pancrealipase for the treatment of postprandial irritable bowel syndrome-diarrhoea. Frontline Gastroenterology, 2:1
3. Nishiyama, H. 2017. Supplementation of pancreatic digestive enzymes alters the composition of intestinal microbiota in mice. 495(1) Biochemical and Biophysical Research Communications.
4. Harvard Medical School. 2016. Can gut bacteria improve your health. Harvard Health Publishing.
5. Hill, C., 2014. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews. Vol 11, 506-514.
6. Gerritsen, J. 2011. Intestinal microbiota in human health and disease: the impact of Probiotics. Genes and Nutrition. Vol 6 No 3

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