fruits and vegetables

Gut Microbiome

*Content has been reviewed by Dr. Elena Comelli (Associate Professor, Department of Nutrition Sciences, University of Toronto) 

  • Understanding the Gut Microbiome. The gut microbiome plays an integral role in overall health but remains a new and emerging area of research. The foods you eat can play a role in the health of the gut microbiome if certain dietary components reach or influence the microorganisms in the large intestine.
  • Sugars and the Gut Microbiome. The role of sugars on the microbiome, especially in humans, is not fully understood and remains an increasing area of research interest. 
  • Dietary Patterns and the Gut Microbiome. Eating a varied and balanced diet that includes fruits, vegetables, whole grains, and fibre-rich foods, may have beneficial effects on the gut microbiome. Prebiotics, probiotics, and synbiotics may also be helpful.

Understanding the Gut Microbiome

The term “gut microbiome” refers to all the microorganisms, the molecules they produce, and their surrounding environmental conditions in the intestinal tract (1,2). Each person’s microbiome is unique (2) and can change due to some or all of the following factors:

  • Age
  • Diet 
  • Drugs and medications 
  • Environment
  • Health status
  • Lifestyle
  • Stress

As the understanding of the gut microbiome continues to advance, it is becoming clearer how certain components of the gut microbiome may impact our health. The composition of our microbiome may affect how nutrients are used in our body for energy as well as the health of the heart and the brain (3). What makes up a healthy gut microbiome is still not well defined (4,5), but research suggests that having a variety of different types of microorganisms that are relatively stable is good for the health of the microbiome (6). The term “dysbiosis” refers to any change in the gut microbiome and is often associated with inflammation and disease (7).  

Sugars and the Gut Microbiome

In general, foods need to reach the large intestine to directly impact the gut microbiome. Sugars are mainly digested and absorbed in the small intestine; however, exceptionally high intakes of sugars, when exceeding the small intestine’s ability to absorb, do reach the large intestine. Therefore, there are many uncertainties as to how they may impact the gut microbiome (8-9). Most research looking at sugars and the microbiome have been animal studies. Human studies are only preliminary and have evaluated different styles of diets (mainly the “Western Diet”) and eating patterns, not the specific effect of sugars (10-11). Although the term “Western Diet” is not well defined, it is generally described as being high in energy, fat, sugars, red meat, and low in fruits, vegetables and dietary fibre. Results of a systematic review suggested that the “Western diet” was associated with dysbiosis and a less favourable gut microbiome compared to a plant-based diet (10). 

Due to increased use of low-calorie sweeteners (such as aspartame, sucralose, and sugar alcohols) in food products, research related to their health impact on the gut microbiome is also on the rise. Low-calorie sweeteners provide a sweet taste with low or no calories. Each low-calorie sweetener is absorbed and/or broken down differently in the body. Stevia, aspartame, sucralose, and sugar alcohols such as sorbitol, xylitol, and mannitol are more likely to reach the large intestine compared to sugars (12). Scientific research has shown some evidence of change in the gut microbiome with the use of low-calorie sweeteners, but these studies need to be interpreted with caution (8, 12) due to high doses in intervention groups, short study durations and small sample sizes. Similar to sugars, few randomized controlled trials to study the effect of low-calorie sweeteners on the microbiome have been conducted in humans. 

Dietary Approaches and the Gut Microbiome

Although a healthy gut microbiome is still not well defined, research suggests that consuming prebiotics and probiotics is beneficial to the microbiome (13,14). Prebiotics travel to the large intestine, where they become the food for the microbiome. Examples of prebiotics include fibres, such as inulin from chicory root, and others found in fruits, cereals, and legumes. Probiotics in comparison are live microorganisms, which benefit the microbiome when consumed in adequate amounts (14). Fermented foods are made through desired microbial growth and enzymatic conversion of food components (15); examples include yogurt, sauerkraut, miso, kimchi, and tempeh. Fermented foods can be consumed for their benefits, and some of them may contain probiotics (15-20). Synbiotics are a combination of carefully selected probiotics and prebiotics that support each other’s functions and may also benefit the microbiome (21).

For optimal gut and overall health, it is important to incorporate a dietary pattern rich in fibre, fruits, vegetables, legumes, whole grains, and sometimes selected probiotics based on specific needs. Further research is needed to gain a better understanding of the impacts of consuming certain dietary components like sugars, low-calorie sweeteners, on the gut microbiome.

For more information about carbohydrate digestion and metabolism: 


  1. Marchesi JR, Ravel J. The vocabulary of microbiome research: a proposal. Microbiome; 2015;3(31). 
  2. Berg G, Rybakova D, Fischer D, Cernava T, Champomier Vergès MC, Charles T, Chen X, Cocolin L, Eversole K, Corral GH, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin JA, Maguin E, Mauchline T, McClure R, Mitter B, Ryan M, Sarand I, Smidt H, Schelkle B, Roume H, Seghal Kiran G, Selvin J, Soares Correa de Souza R, van Overbeek L, Singh BK, Wagner M, Walsh A, Sessitsch A, Schloter M. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020;8(1):103.
  3. Clemente JC, Ursell LK, Parfrey LW, Knight R. The Impact of the Gut Microbiota on Human Health: An Integrative View. Cell. 2012;148(6):1258–70. 
  4. Shanahan F, Ghosh TS, O’Toole PW. The Healthy Microbiome-What Is the Definition of a Healthy Gut Microbiome? Gastroenterology. 2021;160(2):483-94.
  5. McBurney MI, David C, Fraser CM, Schneeman BO, Huttenhower C, Verbeke K, Walter J, Latulippe ME. Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions. J Nutr. 2019;149(11):1882-95.
  6. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489(7415):220-30.
  7. Tomasello G, Mazzola M, Leone A, Sinagra E, Zummo G, Farina F, Damiani P, Capello F, Geagea AG, Jurjus A, Assi TB, Messina M, Carini, F. Nutrition, oxidative stress and intestinal dysbiosis: Influence of diet on gut microbiota in inflammatory bowel diseases. Biomedical Papers. 2016;160(4):461–66. 
  8. Di Rienzi SC, Britton RA. Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners. Adv Nutr. 2019;11(3):616-29.
  9. Townsend GE, Han W, Schwalm ND, Raghavan V, Barry NA, Goodman AL, Groisman EA. Dietary sugar silences a colonization factor in a mammalian gut symbiont. Proc Natl Acad Sci. 2018;116(1):233–38. 
  10. Sen T, Cawthon CR, Ihde BT, Hajnal A, Dilorenzo PM, Serre CBDL, Czaja K. Diet-driven microbiota dysbiosis is associated with vagal remodeling and obesity. Physiol Behav. 2017;173:305–17.
  11. Wilson K, Situ C. Systematic Review on Effects of Diet on Gut Microbiota in Relation to Metabolic Syndromes. J Clin Nutr Metab. 2017;1(2).
  12. Spencer M, Gupta A, Dam LV, Shannon C, Menees S, Chey WD. Artificial Sweeteners: A Systematic Review and Primer for Gastroenterologists. J Neurogastroenterol Motil. 2016;22(2):168–80.
  13. Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD, Verbeke K, Reid G. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14(8):491-502.
  14. Hill C, Guarner F, Reid G, Gibson, GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders M.E. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014;14(8):506-14.
  15. Marco ML, Sandes ME, Ganzel M, Arrieta MC, Cotter PD, De Vuyst L, Hill C, Holzapfel W, Lebeer S, Merenstein D, Reid G, Wolfe BE, Hutkins R. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol. 2021;18:196-208.
  16. Gonzalez S, Fernandez-Navarro T, Arboleya S, de Los Reyes-Gavilan CG, Salazar N, Gueimonde M. Fermented Dairy Foods: Impact on Intestinal Microbiota and Health-Linked Biomarkers. Front Microbiol. 2019;10:1046.
  17.  Park KY, Jeong JK, Lee YE, Daily JW3rd.  Health benefits of kimchi (Korean fermented vegetables) as a probiotic food. J Med Food . 2014;17(1):6-20.
  18. Patra JK, Das G, Paramithiotis S, Shin HS. Kimchi and Other Widely Consumed Traditional Fermented Foods of Korea: A Review. Front Microbiol. 2016;7:1493.
  19. Kok CR, Hutkins R. Yogurt and other fermented foods as sources of health-promoting bacteria. Nutr Rev. 2018;76(Suppl 1):4-15.
  20. Marco ML, Heeney D, Binda S, Cifelli CJ, Cotter PD, Foligné B, Gänzle M, Kort R, Pasin G, Pihlanto A, Smid EJ, Hutkins R. Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol. 2017 Apr;44:94-102.
  21. Swanson, K.S., Gibson, G.R., Hutkins, R., Reimer, R.A., Reid, G, Verbeke K, Scott KP, Holscher, HD, Azad MB, Delzenne NM, Sanders ME. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics. Nat Rev Gastroenterol Hepatol. 2020;17:687-701.