Systemic understanding of microbial interactions and ruminal fermentation

The development of omic approaches has enabled description of the composition of the ruminal microbiota, its genomic potential and its activity with respect to certain targeted functions. However, we still do not know how to precisely describe the function of the ecosystem at the level of the microbiota, to optimise its functioning in the long term or to predict its evolution following different disturbances. With this goal in mind, mathematical modelling offers a powerful tool to better understand the functioning of the ruminal ecosystem. The PhD project aims to improve our understanding of rumen functioning at the systemic scale by developing a multidisciplinary approach that integrates the characterisation of microbial metabolism using omic approaches and the development of models at the genomic scale of bacteria in the rumen. Microbial interactions will be studied in vitro under a “bottom-up” synthetic ecology approach using mini consortia composed of key rumen micro-organisms representing the principal functions of this ecosystem (cellulolysis, amylolysis, proteolysis, methanogenesis) whose genomes are known. The mini consortia tested will be of increasing complexity and supplemented by the yeast Saccharomyces cerevisiae in order to model the effect on microbial activities of this probiotic when used as an additive in animal nutrition.