Comparative genomics of rumen Butyrivibrio 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 genera rumen Butyrivibrio and Pseudobutyrivibrio 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 Butyrivibrio and Pseudobutyrivibrio 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 Butyrivibrio and 6 Pseudobutyrivibrio 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 16S rRNA genes and short-chain fatty acid production have provided insight into the genomic diversity and physiology of these bacteria and divides Butyrivibrio into 3 species clusters. Rumen Butyrivibrio encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 GHs, 1,283 CEs, 110 PLs, 3,605 GTs and 1,706 CBMs with predicted activities involved in the depolymerization and utilization of the insoluble plant polysaccharides were identified. Butyrivibrio 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 Butyrivibrio occupy similar niches but apply different degradation strategies to be able to co-exist in the rumen.