A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory

The rumen microbiota is a unique feature of ruminants and thorough knowledge of the genetic potential of rumen symbiotic microbes provides opportunities for improving the sustainability of ruminant production systems. Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen and constructed 324 high quality metagenomic species. These metagenomic species were prevalent in the rumen of 77 cattle fed different feeds whereas previously identified rumen microbial genomes were less abundant. Compared to human, pig and mouse gut metagenome catalogs, the rumen is richer in functions and microbial species associated to the degradation of plant cell wall material and production of methane. Genes coding for enzymes that deconstruct plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. These data bring new insights on functions, enzymes and microbes of the rumen, critical to understand phenotypes and biological processes.