EggToMeat : Dynamics of bacterial communities throughout the poultry food chain [INRAE ​​exploratory project within the framework of the Holoflux metaprogramme]

The project EggToMeat aims at identifying the impact of farming parameters on the flux of microbiota along the chicken production chain, from eggs to carcasses. For that purpose, two housing conditions (indoors vs outdoor range) will be compared on a single batch of embryonated eggs. Microbiota composition will be determined through gyrB and/or 16S rDNA amplicon sequencing on a longitudinal analysis. The sampling points will encompass egg shells before and just after hatching, chick droppings 2 and 15 days after hatching, just after outdoor access (day 28) and at day 42, and finally, at slaughterhouse (day 63) droppings, ceca and carcasses of individualised chickens. Several zootechnical parameters will also be monitored. A multivariate analysis of the collected data (amplicon sequencing, zootechnical parameters) will be performed to identify microbiota fluxes along the production chain. Impact of outdoor range access on microbiota composition and distribution from eggshells to carcasses will be assessed and correlated to zootechnical parameters. This should enable identifying potential levers shaping microbiota composition. The collected and stored microbiota will be usable for further analyses, as identifying or isolating species or strains of interest. The consortium encompasses the various expertise needed for the project. The collected data and the multidisciplinary work performed during this 1 year project will be the basis to construct a more ambitious project to submit to ANR.