Comparative genomics of rumen uncovers a continuum of polysaccharide-degrading capabilities.

Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera and are important degraders and utilizers of lignocellulosic plant material. These bacteria degrade polysaccharides and ferment the released monosaccharides to yield short-chain fatty acids that are used by the ruminant for growth and the production of meat, milk and fibre products. Although rumen and are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyze the genomes of 40 and 6 strains isolated from the plant-adherent fraction of New Zealand dairy cows to explore the polysaccharide-degrading potential of these important rumen bacteria. Comparative genome analyses combined with phylogenetic analysis of their 16 rRNA genes and short-chain fatty acid production patterns have provided insight into the genomic diversity and physiology of these bacteria and divides into 3 species clusters. Rumen encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 glycoside hydrolases (GHs), 1,283 carbohydrate esterases (CEs), 110 polysaccharide lyases (PLs), 3,605 glycosyl transferases (GTs) and 1,706 carbohydrate-binding protein modules (CBM) with predicted activities involved in the depolymerization and transport of the insoluble plant polysaccharides were identified. genomes have similar patterns of CAZyme families, but vary greatly in the number of genes within each CAZy category, suggesting some level of functional redundancy. These results suggest that rumen occupy similar niches but apply different degradation strategies to be able to co-exist in the rumen. Feeding a global population of eight billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. and are a phylogenetically diverse group of bacteria and are commonly found in the rumen where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings have highlighted the immense enzymatic machinery of and for the degradation of plant fiber, suggesting that these bacteria occupy similar niches but apply different degradation strategies in order to co-exist in the competitive rumen environment.