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Science  —  7 minutes

Understanding your Microbiome

April 12th, 2019
Biron Team
Biron Team

The gut is full of the most wonderful things. We all carry own unique mix of more than 2 kilograms of bacteria in our bowel, as part of a beneficial mix of over 1,000 different species that also includes fungi, yeast, viruses and parasites. Since the day you were born, you’ve carried a thriving, living ecosystem inside of you, and also on your skin, which we call the microbiome.

Though we instinctively think of bacteria and viruses as bad for us, many millions of species exist but only around 1,400 are known to be human pathogens. Every month, new studies are emerging showing just how important the health and diversity of the microbiome is, not just for our digestive health but for our overall wellbeing. The microbiome is critical to our metabolism, it protects us from pathogenic agents, and modulates our immune system. Building on the increasingly common idea of a “gut-brain axis”, promising new studies recently published suggest links between the health of the microbiome and quality of life and even depression and anxiety.

So if my microbiome is so important, how do I look after it?

There’s no such thing as an ideal microbiome you need to achieve. Yours is yours alone, and it has grown and evolved along with you to meet the needs of your body. We’re still learning a lot about what it’s made of, and what helps it thrive, but the basics are a good place to start – your diet, exercise and sleeping patterns will directly impact the composition of your microbiome. Good gut health starts with eating well and looking after yourself.

If you’re sick and taking antibiotics, talk to your doctor about how your prescription may affect your microbiome, and whether that may lead to gastrointestinal symptoms.

As you might expect in such a new and exciting field of understanding of the body, loosely regulated new markets are emerging for both manufactured and more “natural” supplements that promises to give your microbiome a special boost.

Should I take probiotic supplements?

Probiotics are friendly bacteria. They’re a key part of your microbiome, and generally they make their way into your body of their own accord, without any particular help. There are many ongoing research studies underway looking at whether probiotics in supplement form can help fight infections, bowel problems, allergies, and other aspects of your health, but significant benefits have not yet been definitively proven. Some studies have shown benefits, though, including in the control of diarrhea in children[1] or in adults infected with C difficile[2]. However, the large variety of bacteria and their concentrations in currently available probiotics limits generalizing any proven benefit to anything more universal. As the probiotic supplement market is not regulated in the same way medication is – in Canada, probiotics are classified either as foods or as “natural health products” – claims for benefits don’t require the same level of rigorous review. That said, for most people, there’s no real danger to taking probiotics.

Since the composition of everyone’s microbiome is unique, it’s highly unlikely that taking a probiotic containing only a few strains of bacteria will instantly regenerate it completely. A study from an Israeli research group published last year indicated that taking a probiotic after antibiotics will effectively restore a new microbiome but it may actually negatively effect the recovery of your original, complete microbiome[3].

In the meantime, if you are under medical therapy we recommend you always seek the advice of your health professional before taking probiotics. This particularly applies if you are undergoing more serious treatments that may affect your immune system[4].

What are prebiotics? Are those any good?

Prebiotics are ingredients in natural food or supplements that probiotics thrive on, encouraging their growth. Ingredients like inulin or oligofructose (oligosaccharides made of a small number of sugars linked together) or polyphenols will resist acids in the stomach and digestive enzymes in the small bowel and reach the colon where they will be digested and fermented by microorganisms into fuel for the microbiome.

Many natural foods such as whole grains, bananas, greens, onions, garlic, soybeans, and artichokes in your diet will give your gut the fuel it needs. If you don’t eat enough of these foods, you may consider adding prebiotic supplements, even though it will take some time before eventual benefits may be confirmed by the numerous studies currently under way[5].

What about natural sources like yoghurt? Should I drink kombucha?

The “active cultures” on a yoghurt label are referring to probiotics. Good news: the last version of Canada’s Food Guide still recommends two to three serving sizes of dairy products each day including yoghurt and kefir. If you like yoghurt, there’s no harm in eating yoghurt!

Similarly, there are no scientifically proven benefits to drinking kombucha. However, it is true that fermented food and drinks can be an interesting alternative source of bacteria as well as yeasts.

In most circumstances, seeking probiotics from sources such as these won’t be dangerous for your health. If you like the taste of kombucha, it is a nice alternative to drinking sugary soft drinks, but please keep in mind that there have been some serious adverse effects reported from homemade kombucha, possibly due to contamination. Also, don’t bother with kombucha labelled as “pasteurized” if you’re hoping for any probiotic benefit – by definition, all the microorganisms will be dead!


For good digestive health, start with your diet. Follow guides to good nutrition and good sleep, and exercise well. Eat carefully, eat well, look after your body, follow the latest nutrition guidelines, and good gut health and a thriving microbiome will follow.

  1. Cf. Valérie MARCHAND, « L’utilisation des probiotiques au sein de la population pédiatrique », Documents de principe [en ligne], 3 décembre 2012 (mis à jour le 25 février 2019), Ottawa, Société canadienne de pédiatrie,, consulté le 19 avril 2019.

  2. Cf. Ann LÉVESQUE, Jean-Marc DAIGLE et Mélanie TARDIF, « Efficacité et innocuité des probiotiques en prévention des diarrhées associées à Clostridium difficile : revue systématique avec méta-analyses », État des connaissances [en ligne], juin 2017, Québec, Institut national d’excellence en santé et en services sociaux, 58 p.,, consulté le 19 avril 2019.

  3. Cf. Niv ZMORA et al., « Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features », Cell [en ligne], vol. 174, no 6, 6 septembre 2018, Cambridge, Cell Press, p. 1388-1405,, consulté le 19 avril 2019.

  4. Cf. Tina DIDARI et al., « A Systematic Review of the Safety of Probiotics » [en ligne], Expert Opinion on Drug Safety, vol. 13, no 2, 3 janvier 2014, London (UK), Taylor & Francis, p. 227-239,, consulté le 19 avril 2019.

  5. Cf. David A. OSBORN et John KH SINN, « Prébiotiques chez les nourrissons pour la prévention des maladies allergiques et des allergies alimentaires », Cochrane Database of Systematic Reviews [en ligne], vol. 3, 28 mars 2013, Medford, Wiley,, consulté le 19 avril 2019 ; Yves DESJARDINS, « Chaire de recherche industrielle CRSNG-Diana Food sur l’effet prébiotique des polyphénols des fruits et légumes » [en ligne], Profil du titulaire, 20 mai 2014, Québec et Montréal, Science de l’agriculture et de l’alimentation de l’Université Laval et Conseil de recherches en sciences naturelles et en génie du Canada,, consulté le 19 avril 2019

Biron Team
Biron Team