Science — 8 minutes
Probiotics, prebiotics and microbiota

Our gut is populated by incredible little creatures! The digestive system is home to a wide range of micro-organisms totalling more than two kilograms of bacteria in over 1,000 different and beneficial species. Fungi, yeasts, viruses and parasites complete the mix. From the moment we are born, we carry a living, thriving ecosystem in our intestinal tract called the “gut microbiota.”
Bacteria and viruses are mistakenly thought to be harmful, when in fact, out of the millions of species found in nature, about 1,400 are likely to cause disease while the rest are useful. More and more studies are showing that the gut microbiota is an essential player in our health due to its influence on the digestive, metabolic, immune and neurological systems. There is a gut-brain axis (GBA) that suggests a close correlation between microbiota health and several aspects of overall quality of life [1], including depression and anxiety [2]. These same studies also demonstrate the importance of maintaining the balance and diversity of the microbiota [1].
Microbiome or gut microbiota?
The term “gut microbiota” is used to define the vast population of micro-organisms living in our gut, while “microbiome” refers to the collection of chromosome fragments that can be identified in the environment. It is similar in meaning to “genome,” the set of chromosome fragments (genes) in our cells. The term “microbiota,” on the other hand, refers to all the micro-organisms in the same environment (not just their genes). Therefore, it is more accurate to use the term “microbiota” to describe the properties of micro-organisms.
How can I ensure the health of my microbiota?
First of all, it is important to remember that our microbiota is unique, just like our fingerprints. From birth, it grows and evolves at the same pace we do, responding as best it can to our body’s needs. To take care of it, it is best to start early. Contact with the mother (i.e., vaginal delivery, breastfeeding) provides the basic bacteria necessary for the composition of the baby’s initial microbiota. Subsequently, it is enriched through exposure to environmental germs, such as through play and contact with animals. In adulthood, there are three basic components to a balanced microbiota: diet, exercise and healthy sleep habits. Conversely, various factors can weaken the microbiota, such as alcohol abuse and stressful situations [3].
In other words, a healthy gut microbiota starts with good nutrition and self-care. As we are increasingly discovering, the microbiota is a veritable treasure chest that enables us to better understand our body. Yet, as is often the case, these discoveries also mark the emergence of new products (probiotics and prebiotics) that are still largely unregulated, offering supplements to revitalize our microbiota.
Should I take probiotic supplements?
Probiotics are preparations of beneficial bacteria. These mixtures contain only some of the most abundant bacterial strains of a typical microbiota, but unfortunately not all of those that make up a complete microbiota. Several studies are currently under way to determine the full benefits of probiotics ingested in supplement form. However, as probiotic preparations are not standardized, it is difficult to compare the results of these studies.
To date, studies have shown positive effects, particularly for controlling diarrhea and atopic eczema in children, C. difficile infections in adults, and symptoms of irritable bowel syndrome and osteoporosis [4].
In Canada, the sale of probiotics in supplement form is not regulated in the same way as with medications. The marketing of these products requires manufacturers to present evidence of safety, but not efficacy. Despite this, the vast majority of studies have shown that for healthy individuals, there is little real danger in taking probiotics.
Probiotics may be contraindicated, even dangerous, in certain situations, including in people with severe illnesses or compromised immune systems, and premature babies. Some probiotics can lead to infections, unpleasant effects due to certain toxins secreted by the bacteria they contain, or an increase in antibiotic resistance by bacteria already present in our gut [9]. However, in most cases, probiotics from these sources are safe to consume. Kombucha is a good alternative to soft drinks, which are often very high in sugar. However, homemade kombucha sometimes has serious side effects, most likely due to contamination during preparation. Another tip: avoid “pasteurized” kombucha if you want to derive any probiotic benefit from it. By definition, all micro-organisms contained in pasteurized beverages are dead, therefore the desired effect will never materialize.
Moreover, since the composition of each microbiota is unique, it is unlikely that consuming one or a few strains of even useful bacteria from a probiotic can replace the huge variety of micro-organisms that make up our microbiota. For example, the best treatment for a resistant C. difficile infection remains the transplantation of a complete microbiota from the stool of another healthy individual [5]. After a patient’s treatment with antibiotics, however, probiotics can create a temporary base on which other varieties of micro-organisms can be added later [6].
What are prebiotics? Are those any good?
Prebiotics are natural substances or supplements that remain unaltered as they pass through the stomach and small intestine. This allows them to serve as nutrients for certain useful bacteria in the microbiota. The best-known prebiotics are oligosaccharides (a few sugar molecules attached together), such as inulin or oligofructose, and polyphenols. But be careful! As these molecules are fermentable (FODMAPs), they can create problems, such as for people suffering from irritable bowel syndrome [7].
A number of foods are naturally rich in prebiotics, and a good mix of whole grains, bananas, green vegetables, onions, garlic, soy and artichokes in our diet will theoretically give our gut all the prebiotics it should need. If eating these foods is not enough, prebiotics can still be obtained in supplement form. However, we will have to wait for the results of the many studies currently under way before we can determine the usefulness of each type of prebiotic on the market.
What about yogurt and kombucha?
The famous “live cultures” sometimes mentioned on yogurt labels refer to the addition of probiotics. The good news is that the latest version of Canada’s Food Guide still recommends that adults consume two to three servings of dairy products a day, and the list includes yogurt and kefir [8]. If you like these products, keep eating them … sensibly!
Many of the bacteria and yeasts found in fermented foods such as kombucha and yogurt are sensitive to the acids they encounter in the stomach. Theoretically, the higher the concentration of bacteria in a probiotic, the greater the chances that live bacteria will be found in the last segments of our gut. As far as kombucha is concerned, there are no scientifically proven benefits. However, it is true to say that fermented foods and beverages are an alternative, low-sugar source of bacteria and yeast that help build the microbiota. Beware of homemade preparations, which may contain toxic bacteria. Also, pasteurized versions should be avoided: by definition, pasteurization destroys many of the microorganisms contained in the preparation and can eliminate the probiotic effect.
Conclusion
To promote the health of your microbiota, the best way to start is with a healthy diet. We also invite you to follow our advice on good nutrition and a restful sleep. And while you’re at it, don’t forget to exercise regularly.
Sources9
- INSERM. Microbiote intestinal (flore intestinale). Une piste sérieuse pour comprendre l’origine de nombreuses maladies. https://www.inserm.fr/dossier/microbiote-intestinal-flore-intestinale. Consulted March 20, 2025.
- R. G. Xiong, J. Cheng, D. D. Zhou et al. The Role of Gut Microbiota in Anxiety, Depression, and Other Mental Disorders as Well as the Protective Effects of Dietary Components. Nutrients. July 23, 2023, vol. 15, no. 14. doi: 10.3390/nu15143258.
- INRAe. Comment prendre soin de sa symbiose? https://www.inrae.fr/dossiers/microbiote-intestinal-notre-nouvel-allie-sante/comment-prendre-soin-sa-symbiose. Consulted March 21, 2025.
- S. Gul and E. Durante-Mangoni. Unraveling the Puzzle: Health Benefits of Probiotics-A Comprehensive Review. J Clin Med, March 1, 2024, vol. 13, no. 5:1436. doi: 10.3390/jcm13051436.
- John Hopkins Medicine. Fecal Transplant. https://www.hopkinsmedicine.org/health/treatment-tests-and-therapies/fecal-transplant. Consulted March 22, 2025.
- C. Handfield. Probiotiques : oui, non, peut-être? La PressePlus, March 23, 2025. Consulted March 23, 2025.
- Biron Health Group. The low FODMAP diet: A solution for IBS? November 21, 2024. https://www.biron.com/en/education-center/specialist-advice/how-fodmaps-act-on-irritable-bowel-syndrome/. Consulted March 23, 2025.
- Health Canada. 2019 Canada’s Food Guide. https://www.canada.ca/en/health-canada/services/publications/food-nutrition/2019-canada-food-guide-food-classification-system-foods-beverages-categories.html. Consulted March 23, 2025.
- National Institutes of Health (NIH). Probiotics: Usefulness and Safety. https://www.nccih.nih.gov/health/probiotics-usefulness-and-safety. Consulted March 23, 2025.
