Pourquoi avons-nous besoin de bactéries ?

Quelque 100 milliards de bactéries vivent dans et sur notre corps. On en rencontre sur la peau, dans la bouche, le nez, les voies urinaires et les organes sexuels. La plupart d’entre elles habitent les intestins. Les bonnes bactéries de l’intestin sont capables de neutraliser des substances toxiques et d’arrêter les moisissures et les mauvaises bactéries, tout en préservant la santé intestinale et en influençant positivement le système immunitaire.

Microbiote intestinal

Vos intestins abritent des milliards de bactéries, bonnes et mauvaises, formant ensemble le microbiote intestinal. Il en existe au moins mille variétés. Tous les micro-organismes vivant sur et dans notre corps sont appelés collectivement le microbiote. Quant au terme de microbiome, il désigne l’ensemble des gènes de tous ces micro-organismes. Chaque espèce possède sa propre collection de gènes, aussi unique qu’une empreinte digitale ou que notre ADN.

Petits auxiliaires

Certaines bonnes bactéries sont capables de neutraliser des substances toxiques et par exemple de repousser des levures ou des bactéries moins bienveillantes, mais aussi d’influencer positivement le système immunitaire. Les mauvaises bactéries sont également nécessaires d’une certaine façon, à condition de ne pas proliférer à l’excès. Nous avons affaire à un écosystème qui doit rester en équilibre. En fait, cet écosystème dynamique de micro-organismes peut se comparer aux écosystèmes naturels. Tous ses composants doivent fonctionner à l’unisson, dans un équilibre optimal.

Microbiote intestinal

C’est d’autant plus vrai que dans notre corps, les intestins, une machine bien huilée, consacrent 24 heures par jour à digérer les repas, à assimiler les nutriments et à optimiser le système immunitaire. Le microbiote intestinal fabrique notamment les vitamines B et K, ainsi que certains acides gras à chaîne courte qui contribuent à la bonne santé des cellules intestinales.

Maîtrise du système immunitaire

Le siège du système immunitaire se trouve pour une large part dans les intestins. Le microbiote intestinal joue un rôle important à cet égard : il « apprend » au système immunitaire quand il doit intervenir contre des bactéries nocives. Et aussi quand il n’y a pas de raison d’intervenir.

Tout est dans l'équilibre

Plusieurs facteurs peuvent exercer une influence négative sur l’équilibre du microbiote intestinal, notamment une mauvaise alimentation, la maladie, le stress, les voyages ou tout simplement le vieillissement.

Pour le bon équilibre, il importe de manger sain et varié, de se reposer suffisamment, et de surveiller son hygiène, y compris pendant les vacances.

Une alimentation riche en fibres peut vous aider à entretenir un bon niveau de bactéries favorables. On trouve beaucoup de fibres dans des légumes comme les endives et les asperges, dans les fruits, l’avoine et le pain complet.

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Are fermented foods more nutritious?

Yes, fermentation can improve the nutritional content of foods in many ways. Here we explain you how citing tempeh as an example:

Essential Building Blocks

1. Bacteria involved in fermentation produce essential building blocks (vitamins, antioxidants and minerals) that help keeping a healthy body. For instance, dietary sources of vitamin B12 are usually from animal derived foods with very few plants providing a good amount. Lupin beans per se have very little content of vitamin B12 but when fermented by Rhizopus oligosporus and Propionibacterium freudenreichii into tempeh, the content of this vitamin considerably increases making it ideal for vegetarians. 

Neutralizing Anti-Nutrients

2. The process of fermentation “neutralizes” anti-nutrients or digestion blockers. For example, phytic acid is found in many plant products and is known to reduce the digestibility of protein and the release of minerals such as magnesium, iron, calcium and zinc. In short, this acid turns plant food less nutritious. Thanks to the fermentation of soybeans, research demonstrates that Rhizopus oligosporus NRRL 2710 can decrease, in about one third, antinutritional phytic acid in tempeh. The study also show that this microbe can also improve tempeh’s nutritional value by increasing the content of available phosphate.

Diverse Community

3. Fermented foods provide bacteria that contribute to having a diverse community in our gut. A study in healthy volunteers consuming tempeh showed that the participants had an increased population of, amongst others, Akkermansia muciniphila, a bacterium that is naturally present in the intestine and has been actively researched for its benefit in metabolic syndrome.

Can fermented foods cause gas or bloating?

Yes, this could be possible. If what you eat contains live microbes, gas or bloating are part of the most reported side effects, although these are quite harmless. 

Enjoy Small Amounts

Experiencing this kind of discomfort also depends on the amount of fermented foods you are starting with. Enjoy small amounts and allow your gut to go through an adjustment period


Some people do not have problems, others do. When trying to find the source of bloating, it is also important to bear in mind that consuming other, non-fermented foods can also be undigestible to your body, like lactose, and  can also be a common source of bloating.  Your dietician may help you for sure with your detective work to find the cause and the solution.

Can all bacteria in fermented foods survive in the gut?

Not really again. Let’s take fermented milk as an example. Lactic acid-producing bacteria grow on the sugars and other nutrients in milk. As they multiply, the bacteria produce compounds that change the flavour, texture, and yield nutrients in a wide range of products including e.g. cheese or yogurt. 


Many yogurts, but not all, contain bacteria that when consumed can reach the gut alive. When this happens, these bacteria can have an impact on our health as validated by the European Food Safety Agency (EFSA). 

In a scientific opinion, EFSA’s panel on Dietetic Products, Nutrition and Allergies agreed that yogurt containing at least 108 living cells/g  starter cultures of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus improve the digestion of lactose in people with lactose maldigestion

Do all fermented foods contain live microbes?

Not really. To produce fermented foods, ingredients must undergo a transformation process mediated by microbes, either naturally or through the addition of a starter culture. However, some products may afterwards be treated (pasteurized, baked, or filtered) in a way that ultimately kills/removes any live microbes before we consume them.

Heat Treatment

For example, sourdough.  When the dough is used to make bread it will be baked and this exposure to heat will kill the microbes. As well, some fermented vegetables are packaged in jars and may be heat treated as a means of extending its shelf life, or simply to stop the fermentation. Finally, when you prepare e.g. sauerkraut in your kitchen, you probably will be heating it, so you will also kill or inactivate the bacteria.


It may not always be the case for some fermented products to be treated. For those, a very high number of live bacteria will be present at the end of the fermentation.


Yes and no. First of all, let’s recap about what a starter culture is. This is a preparation containing  a high concentration of desired microorganisms that will start and assist a fermentation by making specific chemical, smell and taste changes. Thus, the process becomes efficient, controllable, predictable and… safe!

Happy accidents

Fermented foods were born as “happy accidents” when in the early times suddenly “spoiled” food turned long-lasting and pleasant-tasting. Such accidents were possible thanks to spontaneous or natural fermentation, an event in which you only rely on the microbes present in the environment or the food to colonize the raw materials. If you opt to go for this kind of fermentation, be aware of the risk of contamination. You should take extra care about many aspects such as: acidity, oxygen, temperature, moulds, etc. By not having a proper control over the fermentation, it is possible that you may have an outgrowth of non-friendly microbes in your food. These can produce offflavours or even toxic compounds that can put your health in danger.


Using a starter is not a must but as you can see, it definitely gives you many advantages. This includes a fast acid formation that makes the development of non-desired bacteria much more difficult. What is also important is that, in principle, the quality of commercial starters is checked and you can get information if the microbes present can produce potential compounds that could lead to unpleasant effects including headache, diarrhea, etc.