Holobionts: a new dimension in pig breeding?

Abstract

The role of the microbiota, in particular the gut microbiota, on host performance is increasingly documented in farm animals. These advances have been made possible by the use of new high-throughput sequencing techniques and the development of data-analysis methods to characterize the microorganisms present (diversity, relative abundance, ecosystem assembly). They have provided new insights into the relations between host genetic diversity and host-microbiota interactions, as well as into the estimation of phenotypes or genetic values that consider microbiotic variability. These results fuel a new paradigm based on the definition of the holobiont as a biological system that assembles a host and its microbiota, thus providing a new vision of what an individual represents. We propose to assess the swine holobiont through modelling and experimental results to understand, predict and steer phenotypes to improve, for example, the health but also the productive and environmental efficiencies of pigs. These advances are also discussed as paving the way for developing selection strategies that simultaneously consider information about the host and its microbiota, while reflecting on the sustainable improvement of populations at the scale of a holobiont instead of an individual animal.