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The 7 Best Supplements for Gut Health

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The 7 Best Supplements for Gut Health

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Key Takeaways

  • Several supplements may improve your gut health, including probiotics, prebiotics, omega-3 fatty acids, digestive enzymes, vitamins C and E, beta-carotene, L-glutamine, and ginger.
  • While most research regarding these supplements has been done in animals, studies on humans are starting to emerge. This will lead to more evidence-based recommendations in the future.
  • Lifestyle habits such as diet, exercise and sleep also greatly impact gut health. 

In the last decade, research has shown that gut health and the gut microbiota (sometimes called gut flora) can profoundly impact your overall health.

In response to these findings, there has been an increase in supplements that promise to pave the way to better gut health.

Read on to learn about the research behind the best gut health supplements, side effects to watch out for, and other tips to promote gut health.


Can Supplements Help Improve Gut Health?

While the research is still emerging, early studies show that certain supplements can improve gut health, particularly if you have a gastrointestinal disorder like irritable bowel syndrome (IBS). 

What Supplements Improve Gut Health?

Here are seven of the best gut health supplements currently available.

Discuss supplement use with your healthcare provider prior to starting a regime, as some supplements could interact with other medications or supplements you may already be taking.


Probiotics are live microorganisms that, when taken in adequate amounts, provide benefits to human health.

Probiotics have been shown to help with several digestive problems, including antibiotic-associated diarrhea, constipation, and irritable bowel syndrome.

Antibiotic-associated diarrhea: A recent meta-analysis showed that using probiotics as soon as possible during antibiotic therapy effectively prevented antibiotic-associated diarrhea in adults.

Constipation: A systematic review and meta-analysis found that Bifidobacterium lactis significantly increased the frequency of bowel movements and constipation symptom scores. 

Irritable bowel syndrome: A systematic review and meta-analysis found that probiotics significantly increased the frequency of bowel movements and improved bowel movement consistency for people with constipation-predominant IBS. Another study found that a mixture of Lactobacillus, Bifidobacterium, and Streptococcus thermophilus significantly improved symptom severity in people with diarrhea-predominant IBS. 

Since different strains of probiotics treat different symptoms, choosing the correct strain is important. Your doctor or dietitian can help you choose the correct strain to manage your symptoms.


Prebiotics are indigestible compounds that can stimulate certain microorganisms' growth and activity.

When the gut microbes ferment prebiotics, metabolites are created.

These byproducts have several beneficial effects on gut health, such as regulating the immune system, resisting harmful microorganisms, improving the function of your gut barrier, and acting as a fuel source for your gut cells. 

Omega-3 Fatty Acids

Omega-3 fatty acids are essential fatty acids–we must get them through our diet.

The most common omega-3 fatty acids are eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and alpha-linolenic acid (ALA). 

EPA and DHA are found in fatty fish like salmon and mackerel, while ALA is found in certain plant foods such as flaxseed. Only a small amount of ALA can be converted to EPA and DHA, so supplements are often required if a person doesn’t eat much fish.

Emerging evidence suggests there is a connection between omega-3 fatty acids and gut microbiota. It’s thought that omega-3 fatty acids affect the gut microbiota by:

  1. Influencing the type and amount of gut microbes.
  2. Altering the levels of compounds associated with inflammation.
  3. Regulating the levels of short-chain fatty acids (SCFAs). SCFAs are anti-inflammatory compounds that act as an energy source for the cells of the large intestine.


Digestive Enzymes

Digestive enzymes help break down food to promote healthy digestion.

If you don’t have enough of certain digestive enzymes, your body may have trouble breaking down certain foods.

One of the most common digestive enzyme deficiencies is lactose intolerance.

In this case, their body doesn’t produce enough lactase, the enzyme that breaks down lactose found in dairy products. For these people, taking digestive enzymes (specifically, lactase) before eating dairy products can improve gut health by reducing the symptoms of lactose intolerance.

Emerging research also shows that digestive enzymes could help people with IBS. Galactooligosaccharides (GOS) can trigger symptoms in people with IBS.

A small study found that supplemental alpha-galactosidase (the enzyme needed to break down GOS) resulted in reduced overall symptoms and bloating for people with IBS who ate foods containing GOS.

Antioxidants and Vitamins

Vitamin C, vitamin E, and beta-carotene (which is converted into vitamin A in the body) are antioxidant vitamins that can be obtained through a person’s diet.

Studies show that these vitamins can alter the composition and metabolic activity of the gut microbiota, leading to improved intestinal barrier function and an immune system that functions normally.


L-glutamine is an amino acid that acts as a building block for your cells.

It promotes the growth of cells in the intestines, controls the “leakiness” of the gut wall, and reduces inflammation. 

A small study looked at the effects of L-glutamine supplementation during the low FODMAP diet for people with IBS.

They found that L-glutamine supplementation significantly reduced IBS symptoms when combined with the low FODMAP diet.

It remains to be seen whether L-glutamine supplementation benefits people with other gastrointestinal disorders or if it is useful for general gut health.


Ginger has been used in traditional medicine to treat gut-related problems for centuries.

It’s a well-established antioxidant, has anti-inflammatory properties, and is commonly used to treat nausea and vomiting.

A small study looking at the effects of ginger juice found that when it was consumed, it increased the number of species of bacteria in the gut and changed the relative abundance of several types of bacteria. 

Of particular note, the abundance of Ruminococcus, a bacteria that promotes inflammation, decreased, while the abundance of Faecalibacterium, a bacteria that produces anti-inflammatory compounds, increased. 

While it remains to be seen whether this translates to improved gut health, emerging evidence suggests that ginger could be an effective gut health supplement.

Side Effects of Taking These Supplements

It’s important to be aware of common side effects of supplements for gut health. Here are some of the most common side effects:

  • Probiotics: Probiotics typically don’t produce many side effects. You may sometimes experience gas, bloating, belching, and flatulence. If your probiotics are yeast-based, they may cause constipation. However, these symptoms are usually mild.
  • Prebiotics: The most common side effect of prebiotics is gas and bloating. Prebiotics may also produce abdominal pain and diarrhea if taken in large doses.
  • Omega-3 Fatty Acids: Omega-3 fatty acid supplements may produce mild symptoms such as an unpleasant taste in your mouth, bad breath, bad-smelling sweat, headaches, heartburn, nausea, and diarrhea.
  • Digestive Enzymes: Lactase and alpha-galactosidase do not typically produce any side effects. 
  • Antioxidants and Vitamins: Taking vitamins in high doses may have unwanted side effects. Antioxidant vitamins, such as vitamin C and vitamin E, may reduce the effectiveness of certain types of chemotherapy. Too much vitamin A can cause headaches, liver damage, and birth defects.
  • L-Glutamine: L-glutamine supplementation may cause constipation, nausea, headaches, abdominal pain, cough, or pain in your back, legs, feet, hands, or arms. If symptoms don’t go away on their own, call your doctor.
  • Ginger: Side effects of ginger supplementation include abdominal discomfort, heartburn, diarrhea, and mouth and throat irritation. This typically occurs when ginger is taken in large doses.

Other Ways to Support Gut Health

While the research on the best gut health supplements is promising, it’s important to have other ways to nourish your gut. This includes eating more plant-based foods, exercising regularly, and maintaining good sleep habits.


Studies show that following a plant-based diet high in fiber leads to a shift in the gut microbiota that could protect against developing inflammatory bowel disease (IBD).

This doesn’t mean you need to cut out animal products completely. Rather, focus on all the delicious plant-based foods you can ADD to your diet. 


Exercise has been shown to reduce your risk of colon cancer, diverticulosis, and inflammatory bowel disease. It may also reduce inflammation and protect the integrity of the gut lining.

A study of elite rugby players found that exercise enhanced gut microbiota diversity.

Overall, exercise appears to be an accessible and effective way to improve gut health.


A small recent study found that people who got better sleep had more diversity in their gut microbiota.

Since diversity is a marker of a healthy gut microbiota, getting enough sleep could be a key component of maintaining gut health.


There are a lot of gut health supplements out there, but the best gut health supplements are the ones with scientific evidence to support their use.

While most supplements don’t cause severe side effects, discussing their use with a trusted healthcare provider is important, as some supplements could interfere with other medications or supplements you may be taking.

How a Gut Health Dietitian Can Help

If you’re considering taking supplements or changing your diet to support gut health but aren’t sure where to start, consider working with a registered dietitian nutritionist.


Frequently Asked Questions

What is the best supplement for a healthy gut?

The best supplement for a healthy gut is a supplement with science to back up its use. Some of the most popular evidence-based supplements for a healthy gut include probiotics, prebiotics, omega-3 fatty acids, vitamin C, vitamin E, beta-carotene, and L-glutamine.

Are gut health supplements worth it?

Overall, gut health supplements may only be worth it if you have a specific gut-related problem to treat (for example, irritable bowel syndrome). If you’re an otherwise healthy person simply looking to improve your overall health, strategies such as eating ample plant-based foods, exercising regularly, and getting enough sleep are likely enough to keep your gut happy and healthy.

Can I reset my gut lining?

Depending on the cause of your gut lining problems, you may be able to reset it. For example, your gut lining may be damaged if you have celiac disease and have been eating gluten. Eliminating gluten will give your gut lining a chance to heal and reset.

Another situation in which your gut lining may be impaired is if you are not consuming enough L-glutamine. Since L-glutamine regulates the “leakiness” of the gut, not getting enough could harm your gut lining. In this case, taking an L-glutamine supplement may help “reset” your gut.


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