Application of rumen microbial genome information to livestock systems in the postgenomic era
G. T. Attwood A B , W. J. Kelly A , E. H. Altermann A , C. D. Moon A , S. Leahy A and A. L. Cookson AA Food, Metabolism & Microbiology Section, Food and Textiles Group, AgResearch, Grasslands Research Institute, Palmerston North, New Zealand.
B Corresponding author. Email: graeme.attwood@agresearch.co.nz
Australian Journal of Experimental Agriculture 48(7) 695-700 https://doi.org/10.1071/EA07408
Submitted: 11 December 2007 Accepted: 6 March 2008 Published: 20 June 2008
Abstract
Sequencing the genomes of individual rumen microbes and determining the function of their encoded genes promises to transform our understanding of the microbiology of the rumen. The diversity and density of microbes in the rumen, and our inability to culture the majority of rumen microbes, limit current genome studies to only a small fraction of the microbes present in this environment. Nevertheless, genomes of fibre-degrading organisms are beginning to reveal a previously unexpected abundance of genes encoding glycosyl hydrolases and carbohydrate esterases, which could be used to enhance fibre digestion in the rumen. Additionally, genome sequencing of a rumen methanogen is identifying conserved genes within the methanogenic archaea that may serve as targets for their inhibition and therefore reduction of methane emissions from ruminants. The problem of rumen microbe culturability can be overcome by a new approach called metagenomics, in which microbial DNAs are extracted from rumen samples and sequenced independent of cultivation. In the future, sequencing individual genomes and metagenomic libraries is likely to capture much more of the microbial DNA in the rumen and, coupled with postgenomic studies on gene and protein expression, is likely to enhance our knowledge of the microbial component of ruminant digestion.
Acknowledgements
Gratitude is expressed to Dong Li, Zhanhao Kong, Hassan Hussein, Jonathan Dunne, and Jude Bond for their contributions to this work. The Clostridium proteoclasticum genome sequencing project was funded by the New Economy Research Fund of the New Zealand Foundation for Research Science and Technology and the Methanobrevibacter ruminantium genome project was funded by the Pastoral Greenhouse Gas Research Consortium.
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