Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities

Palevich, Nikola; Kelly, William J.; Leahy, Sinead C.; Denman, Stuart; Altermann, Eric; Rakonjac, Jasna; Attwood, Graeme T.

doi:10.1128/aem.01993-19

Title: Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities

Journal Article · Fri Dec 13 00:00:00 EST 2019 · Applied and Environmental Microbiology

DOI:https://doi.org/10.1128/aem.01993-19· OSTI ID:1626066

Palevich, Nikola ^[1]; Kelly, William J. ^[2]; Leahy, Sinead C. ^[1]; Denman, Stuart ^[3]; Altermann, Eric ^[1];

^[4]; Attwood, Graeme T. ^[1]

AgResearch Limited, Palmerston North (New Zealand)
Donvis Limited, Palmerston North (New Zealand)
Agriculture and Food (CSIRO), St. Lucia, QLD (Australia)
Massey Univ., Palmerston North (New Zealand)

Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera 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 fiber products. Although rumen Butyrivibrio and Pseudobutyrivibrio species are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyzed 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 patterns provide insight into the genomic diversity and physiology of these bacteria and divide Butyrivibrio into 3 species clusters. Rumen Butyrivibrio bacteria were found to 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 glycosyltransferases (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. Butyrivibrio genomes had similar patterns of CAZyme families but varied greatly in the number of genes within each category in the Carbohydrate-Active Enzymes database (CAZy), suggesting some level of functional redundancy. These results suggest that rumen Butyrivibrio species occupy similar niches but apply different degradation strategies to be able to coexist in the rumen.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); New Zealand Ministry of Business, Innovation and Employment New Economy Research Fund; New Zealand Government

Grant/Contract Number:: AC02-05CH11231; C10X0803

OSTI ID:: 1626066

Journal Information:: Applied and Environmental Microbiology, Vol. 86, Issue 1; ISSN 0099-2240

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 40 works

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