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EnglishThe gastrointestinal microbiota is a symbiont deeply involved in the physiology of its host through the regulation of digestion, metabolism and immunity and consequently in the host adaptability to changing environments. In particular, the role of the gastrointestinal microbiota in maintaining host health is important and has been under-estimated until now. It is an inherent component of the animal that should be described when phenotyping animals. The rapid development of high throughput sequencing technologies facilitates its composition, diversity and stability over time and the measure of its variability according to different factors such as genotype, nutrition and breeding conditions. This kwoledge should allow defining the properties of a "normal" gastrointestinal microbiota associated with health, identifying the microbiota dysfuctions and understanding their consequences or host physiology. It will lead tho the identification of diagnostic and pronostic markers for gastrointestinal dysbiosis thus furnishing new tools for promoting health. Finally, the manipulation of the gastrointestinal microbiota will constitute a way to better adapt animals to their environment by improving their robustness, limit the use of antibiotics and improve food safety by preventing the development of bacteria threatening human health. Due to the high quantity of data to be acquired and analyzed, achieving these objectives for each species of interest remains a challenge. francaisLe microbiote digestif est un symbionte dont on a demontre l'implication essentielle dans la regulation de la physiologie de l'hote qui l'heberge pour la digestion, le metabolisme et l'immunite. Ce microbiote a en particulier un role majeur, et jusqu'ici sous-estime, sur la sante de son hote et participe a son adaptabilite a des environnements changeants. Les technologies de sequencage a haut debit devraient faciliter l'inclusion de cet ecosysteme complexe dans le phenotypage des animaux d'elevage. Ce connaissances devraient permettre de definir les proprietes d'un microbiote digestif "normal" associe a une bonne sante, d'en preciser les dysfonctionnements et de comprendre leurs repercussions sur l'etat de sante de l'animal. Cela conduira a identifier des marqueurs de diagnostic et de pronostic de ces dysfonctionnements, fournissant des moyens de controle nouveaux de la sante en elevage, apprehendee en terme d'optimisation des rendements de production, de resistance aux maladies et de maintien du bien-etre. A terme, le controle du microbiote digestif par l'alimentation, la genetique ou les pratiques d'elevage en ameliorant leur robustesse, de limiter l'utilisation d'antibiotiques et de preserver la securite sanitaire des aliments en evitant le developpement de bacteries pathogenes pour l'Homme. L'ampleurs des donnees a generer et a analyser pour les differentes especes d'interet reste le defi a relever.

inra productions animales

Intégrer la caractérisation du microbiote digestif dans le phénotypage de l’animal de rente : vers un nouvel outil de maîtrise de la santé en élevage ?