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Integrating the characterization of digestive microbiota in phenotyping livestock animals: towards a new tool for animal health control?

INRA Prod Anim 27(3) 209-222


1 INRA, UMR1313 GABI, F-78352 Jouy-en-Josas, France

2 AgroParisTech, UMR1313 GABI, 16 rue Claude Bernard, F-75321 Paris, France

3 INRA, UMR1213 Herbivores, F-63122 Saint-Genès-Champanelle, France

4 Université de Clermont-Ferrand, VetAgro Sup, UMR1213 Herbivores, F-63000, Clermont-Ferrand, France

5 INRA, UMR1348 PEGASE, F-35590 Rennes, France

6 Agrocampus Ouest, UMR1348 PEGASE, F-35000 Rennes, France

7 INRA, UMR1282 ISP, F-37380 Nouzilly, France

8 Université François Rabelais, UMR1282 ISP, F-37200 Tours, France


The 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 the description of this complex ecosystem in livestock species. For each animal species, its description should include the measure of 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 knowledge should allow defining the properties of a ‘normal’ gastrointestinal microbiota associated with health, identifying the microbiota dysfunctions and understanding their consequences on host physiology. It will lead to the identification of diagnostic and prognostic 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.

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