A catalogue of the pig gut microbiome

The pig is a major species for livestock and biomedicine. We established a comprehensive catalogue of gut microbial genes based on faecal samples of 287 pigs from France, Denmark and China. 7.7 million non-redundant genes representing 719 metagenomic species were identified by deep metagenome sequencing. The pig and human catalogues share 12.6 % and 9.3 % of their genes, respectively, a higher proportion than that shared between the mouse and human catalogues. Importantly, 78 % and 96% of the functional pathways are shared, underscoring the potential use of pigs for biomedical research. The pig gut microbiota is influenced by gender, age and breed. Analysis of the prevalence of antibiotic resistance genes confirmed the efficiency of eliminating antibiotics from animal diet to reduce the risk of dissemination associated with farming systems. The pig microbiome gene catalogue provides a useful resource for metagenomics-based research in biomedicine and for sustainable knowledge-based pig farming.