Identification of microbial species and genes associated with the bovine rumen and understanding their relationship to host feed efficiency

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We hypothesize that variation in feed efficiency (the ability of an individual to extract energy from its food) among cattle is mediated in part by differences in the composition of the rumen microbial community, because of the role of rumen bacteria in fiber digestion, the observation that additives that alter the composition of the rumen microbial population affect feed efficiency, and increasing evidence from other species that gut bacteria affect host traits such as obesity. We will explore the relationship between rumen bacteria and feed efficiency using both a species-centric and a gene-centric approach. The species-centric approach will involve isolating and sequencing a particular gene (called cpn60) from rumen bacteria, to estimate how many distinct bacterial species are present and to estimate their abundance. The gene-centric approach will involve extensive sequencing of random genome fragments isolated from rumen bacteria. We will use a variety of computational approaches to analyze the genome fragment sequences, to predict their functional properties and to identify the metabolic processes they support. The species- and gene-centric approaches will be applied to high feed efficiency individuals and to low feed efficiency individuals. The types and abundance of bacterial species, gene functions, and metabolic processes will be compared, to identify those that are associated with high feed efficiency. Long-term research will focus on understanding the mechanisms by which the bacterial species and genes we identify affect feed efficiency. The work described in this proposal will increase our understanding of the structure and physiology of the rumen microbial ecosystem. In addition to providing new diversity estimates for the rumen microbial community, this study has the potential to reveal novel species; unexpected protein families and metabolic functions; and new enzymes of biotechnological importance. Of particular practical interest will be microbial species or genes found to be associated with high feed efficiency. Knowledge of these species and genes may eventually lead to more efficient animals that produce fewer greenhouse gases, and reduced feed costs for Canadian livestock producers.