Microbiomes As Actors of Host Phenotype Variability: An Increasing Research Field in Animal Biology

Evidence of the contribution of gastrointestinal microbiota to animal health and performance, including the metabolism of nutrients, stimulation of immune response, protection from pathogens and stimulation of epithelium cell proliferation, is increasingly important. Microbiomes interplay with their hosts and more and more studies aim at deciphering the links between microbiota composition and host phenotype variability. We will illustrate this emerging field in farmed animals by presenting results on pigs with a focus on the first gene catalogue of the gut microbiota recently established in this species by a joint initiative from INRA (France), BGI-Shenzhen (China) and the University of Copenhagen (Denmark). By deep metagenome sequencing of fecal DNA from 287 pigs, we identified 7.7 million non-redundant genes representing 719 metagenomic species. Among the functional pathways found in the human catalogue, 96% are present in the pig catalogue, which supports the potential use of pigs for biomedical research. Our findings suggest that sex, age and host genetics may affect the pig gut microbiome. Analysis of the prevalence of antibiotic resistance genes demonstrated the effect of eliminating antibiotics from animal diets and thereby reducing the risk of spreading antibiotic resistance associated with farming systems. The pig microbiome gene catalogue will be discussed as a new resource to implement metagenomics-based studies, thus providing unprecedented research capacity to deeply study host microbiome interplay in pigs for biomedical research as well as knowledge-based pig farming.