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What are the best foods for gut health?

The average human gut contains approximately 300-500 different species of bacteria, with 500+ different species in the lower large intestine alone.1

The number of bacteria living in our intestines is roughly ten times the total number of cells in our entire body!2

These bacteria are not all good – some are bad bacteria that can seriously harm our health if found in high populations. Altering our diets can enhance the growth of beneficial bacteria in our gut, helping us combat certain diseases and abdominal discomfort.

What are the best foods for gut health?

Good gut bacteria include those that produce vitamin K, which is used in the blood clotting process.

The gut microbiome also helps facilitate efficient fat metabolism and plays an important role in protecting against harmful pathogens.

How do we know if we have a healthy gut?

A key indicator of a healthy gut is a regular bowel movement.

However, if regular bowel movements include diarrhea or constipation, this may indicate an unhealthy gut. Experts also warn that abdominal pain, excessive gas, and bloating can indicate poor gut health.

If you experience daily abdominal discomfort or irregular bowel movements, you may benefit from a microbiome boost.

Incorporating certain foods into the diet can help build a strong symbiotic microbiome.

Foods that promote a healthy gut

Dietary fibre

Fibre is a carbohydrate that humans actually cannot digest – but the bacteria in the gut can.

Some gut bacteria actually use soluble fibre as an energy source, promoting bacterial growth and enhancing the immunity of the digestive system.

Insoluble fibre, such as the fibre found in cereals and wheat grains, is not digested by bacteria.3

This fibre retains water in the stool and has been shown to increase the size of bowel movements, increase stool output and cause a faster rate of stool passage through the gut.

One study reported that a high intake of fibre from cereal and whole grains significantly reduced the risk of colorectal cancer.4

A similar study looked at the relationship between fibre intake and colon health.

They found that age, biological sex, lifestyle, and other dietary variables did not affect the decreased colorectal cancer risk observed with increased dietary fibre intake.5

The study also found that dietary fibre from fruits, vegetables, and cereals helped reduced the risk of colon cancer, but only cereal fibre significantly reduced the risk of rectal cancer.5


Certain vegetables can make your gut feel better than others.

Vegetables that are “inulin-rich” contain inulin-type fructans which are fermentable dietary fibre.

Such inulin-containing vegetables include asparagus, garlic, leeks, bananas, and chicory root. A study took 26 healthy individuals and put them on an inulin-rich diet for two weeks.

The researchers observed an increase in the gut bacteria Bifidobacterium, which has been associated with increased flatulence, as was experienced by the study participants.6

They also observed a decrease in another type of bacteria associated with intestinal discomfort.

The individuals also showed increased feelings of fullness and a reduced desire to eat salty, sweet, and fatty foods.

Another study reported that prebiotics like the fructans in high-inulin vegetables was associated with increased production of gut peptides that contribute to the feeling of being full.7


Some of our gut microbes need nitrogen as an energy source.

Dietary protein acts as a major source of nitrogen for these bacteria to properly function.

With nitrogen, these bacteria produce short-chain fatty acids, which are required by some other bacteria and colorectal tissue for energy.8

But are all protein sources beneficial to gut health?

Red meat contains a carbohydrate compound that we cannot produce ourselves. Studies have shown that when we consume red meat, our immune system recognizes this compound as foreign material.

The resulting immune system response leads to inflammation, which has been shown to contribute to colorectal cancer 9 and atherosclerosis.10

One of the health benefits of our gut microbiome is that some bacteria produce enzymes that help break down this compound, preventing inflammation.11

Another study looked at whether the temperature at which red meat is cooked alters the severity of the inflammation and cell damage.

In particular, they studied colorectal cell DNA damage in meat cooked at high versus low temperatures.

Their findings suggest that meat cooked at higher temperatures may increase the risk of colorectal adenoma, a benign mass in the colon that can be a precursor for colon cancer.12

They observed that when cruciferous vegetables and yogurt were added to a high-temperature meat diet, the mutagenicity, or risk for colorectal cancer, decreased.


Prebiotics promotes bacterial growth.

A study took 10 healthy individuals and gave half of them 16g/day of prebiotics for two weeks.

They observed that bacteria fermentation increased by an approximate factor of three.7 They also observed a significant increase in levels of gut-secreted peptides called peptide 1 and peptide YY.

High levels of these peptides contribute to appetite regulation and satiety.

Prebiotics can be consumed as a supplement or are found in relatively high concentrations in chicory root, wheat bran, and barley.


Probiotics are live strains of bacteria that add to the bacterial population in your gut.

Yogurt contains lactic acid-producing bacteria called Lactobacillus acidophilus that bind to a specific type of bacteria in the gut.

One study observed that in the presence of L. acidophilus, the bacteria that cause diarrhea were less able to bind to the gut lining to cause infection.13

They concluded that there is a dose-dependent relationship between this probiotic and increased gut immunity against pathogens.

What if you have a health condition or a strict diet?

How should your diet change to promote optimal gut health?

Irritable bowel syndrome (IBS)

IBS is characterized by gastrointestinal discomfort including excessive bloating, abdominal pain, diarrhea, flatulence, and constipation.

Health professionals do not know exactly what causes IBS, but the newly developed low-FODMAP diet has shown promise in alleviating IBS symptoms.  

The low FODMAP diet

FODMAPS are fermentable carbohydrates.

Although fermented foods can be good for promoting bacterial growth, they can contribute to the symptoms of IBS.

Medical researchers have been following the success of the low FODMAP in individuals with IBS, and it has been reported that up to 86% of patients with IBS had overall improved gastrointestinal comfort and functioning while on the diet.14

However, studies have also shown that a low FODMAP diet risks nutritional deprivation and can harm gut bacteria.15

Healthcare professionals suggest that decreasing FODMAP foods may help alleviate IBS symptoms, but FODMAPS should not be eliminated completely.

This risk of insufficient nutrition has led researchers to investigate the gluten-free diet as an alternative IBS treatment.

Gluten-free diet

Some individuals with IBS have been recorded as trying a gluten-free diet because gluten has been linked to similar bowel symptoms.

One study took 41 patients with IBS and put them on a gluten-free diet for six weeks.

After six weeks, 71% of patients experienced a significant reduction in IBS symptoms.16

Inflammatory bowel disease (IBD)

IBD includes ulcerative colitis and Crohn’s disease. Both can seriously damage health by limiting nutritional intake and causing severe weight loss.

One study found that those with infectious colitis and irritable bowel disease had lower levels of a type of bacteria that normally helps protect gut mucus and normal bowel function.17

According to the Crohn’s and Colitis Foundation, the best foods for gut health for those with IBD includes low-fibre fruits such as cantaloupe and melon, lean protein, and non-cruciferous vegetables.18

Lactose intolerance

If you are lactose intolerant, you lack the ability to fully digest a type of sugar, lactose, commonly found in dairy products.

Dairy is not one of the best foods for gut health in lactose-intolerant individuals because it can lead to severe bloating, diarrhea, and abdominal discomfort.

As such, these foods should be avoided.  

Vegan & vegetarian diets

Research has shown that a diet high in plant-based foods tends to induce a more diverse and stable gut microbiome.

Plant-based foods tend to have a high fibre content, contributing to the production of short-chain fatty acids which play a part in the intestine function.

Individuals who consume a high plant-based diet also tend to eat more polyphenols, which help strengthen the immune system against pathogens and inflammation.19

Vegans and vegetarians have significantly higher counts of Bacteroidetes than omnivores, which has been found low in IBD patients.20

This research suggests that the higher vegetable consumption seen in vegans and vegetarians strengthens gut health.

Experts advise that a strict vegan/vegetarian diet is not necessary to achieve these benefits, as long as the omnivore diet is high in plant products.

The best foods for gut health will vary depending on personal health and diet restrictions.

Studies have suggested that for a healthy individual, consuming dietary fibre, lean protein, prebiotics, and probiotics can assist in maintaining gut health.

Rich foods such as fried foods, are more difficult to digest and may disrupt gut health.

Individuals with health conditions such as IBS or IBD may need to search for low-fibre and low-FODMAP foods to ease symptoms.

Each person’s optimal gut-friendly diet will differ depending on dietary restrictions and other bowel-related diseases, and as such, online dietary suggestions should be used for informational purposes only.

Speak with your healthcare provider to better understand how to optimize your gut health.


  1. Evaldson, G. et al. (1982). The normal human anaerobic microflora. Scandinavian Journal of Infectious Diseases. Supplementum; 35: 9-15.
  2. Quigley, E.M.M. (2013). Gut Bacteria in Health and Disease. Gastroenterology & Hepatology; 9(9): 560-569.
  3. Stephen, A.M. and J.H. Cummings. (1980). Mechanism of action of dietary fibre in the human colon. Nature; 284(5753): 283-284. Doi: 10.1038/284283a0.
  4. Aune, D. et al. (2011). Dietary fibre, whole grains, and risk of colorectal cancer: systematic review and dose-response meta-analysis of prospective studies. British Medical Journal; 343: d6617. Doi: 10.1136/bmj.d6617.
  5. Murphy, N. et al. (2012). Dietary fibre intake and risks of cancers of the colon and rectum in the European prospective investigation into cancer and nutrition (EPIC). PLoS One; 7(6): e39361. Doi: 10.1371/journal.pone.0039361.
  6. Hiel, S. et al. (2019). Effects of a diet based on inulin-rich vegetables on gut health and nutritional behaviour in healthy humans. The American Journal of Clinical Journal; 109(6): 1683-1695. Doi: 10.1093/ajcn/nqz001.
  7. Cani, P.D. et al. (2009). Gut microbiota fermentation of prebiotics increases satietogenic and incretin gut peptide production with consequences for appetite sensation and glucose response after a meal. The American Journal of Clinical Nutrition; 90(5): 1236-1243. Doi: 10.3945/ajcn.2009.28095.
  8. Conlon, M.A. et al. (2015). The impact of Diet and Lifestyle on Gut Microbiota and Human Health. Nutrients; 7(1): 17-44. Doi: 10.3390/nu7010017.
  9. Alisson-Silva et al. (2016). Human risk of diseases associated with red meat intake: Analysis of current theories and proposed role for metabolic incorporation of a non-human sialic acid. Molecular Aspects of Medicine; 51: 16-30. Doi: 10.1016/j.mam.2016.07.002.
  10. Kawanishi, K. et al. (2019). Human species-specific loss of CMP-N-acetylneuraminic acid hydroxylase enhances atherosclerosis via intrinsic and extrinsic mechanisms. Proceedings of the National Academy of Sciences of the United States of America; 116(32): 16036-16045.
  11. Zaramela, L.S. et al. (2019). Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates. Nature Microbiology; 4(12): 2082-2089. Doi: 10.1038/s41564-019-0564-9.
  12. Shaughnessy, D.T. et al. (2011). Inhibition of Fried Meat-Induced Colorectal DNA Damage and Altered Systemic Genotoxicity in Humans by Crucifera, Chlorophyllin, and Yogurt. PLoS One; 6(4): e18707. Doi: 10.1371/journal.pone.0018707.
  13. Bernet, M.F. et al. (1994). Lactobacillus acidophilus LA 1 binds to cultured human intestinal cell lines and inhibits cell attachment and cell invasion by enterovirulent bacteria. Gut; 35(4): 483-489.
  14. Nanayakkara, W.S. et al. (2016). Efficacy of the low FODMAP diet for treating irritable bowel syndrome: the evidence to date. Clinical and Experimental Gastroenterology; 9: 131-142. Doi: 10.2147/CEG.S86798.
  15. Hill, P. et al. (2017). Controversies and Recent Developments of the Low-FODMAP Diet. Gastroenterology & Hepatology; 13(1): 36-45.
  16. Aziz, I. et al. (2016). Efficacy of a Gluten-Free Diet in Subjects With Irritable Bowel Syndrome-Diarrhea Unaware of Their HLA-DQ2/8 Genotype. Clinical Gastroenterology and Hepatology; 14(5): 696-703. Doi: 10.1016/j.cgh.2015.12.031.
  17. Sokol, H. et al. (2009). Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflammatory Bowel Diseases; 15(8): 1183-1189. Doi: 10.1002/ibd.20903.
  18. What Should I Eat? (n.d.). Crohn’s & Colitis Foundation. Accessed on Apr. 10 2021. Retrieved from
  19. Tomova, A. et al. (2019). The Effects of Vegetarian and Vegan Diets on Gut Microbiota. Frontiers in Nutrition; 6: 47. Doi: 10.3389/fnut.2019.00047.
  20. Zhou, Y. and F. Zhi. (2016). Lower Level of Bacteroides in the Gut Microbiota Is Associated with Inflammatory Bowel Disease: A Meta-Analysis. BioMed Research International; 2016. Doi: 10.1155/2016/5828959.

Image by congerdesign from Pixabay 

Bryn Evans
Bryn Evans
I graduated with a major in biochemistry, a minor in physics, and a certificate in business from Queen’s University. My long-term goal is to become a family physician (MD) and earn a Master’s in Public Health (MPH). I am passionate about public health, mental health, & wellness. I'm currently completing a Certificate in Effective Writing for Healthcare because I recognize how important it is to communicate effectively with the public!


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