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United States Department of Agriculture

Agricultural Research Service

Research Project: EPIDEMIOLOGY, PATHOGENESIS AND COUNTERMEASURES TO PREVENT AND CONTROL ENTERIC VIRUSES OF POULTRY

Location: Endemic Poultry Viral Diseases Research Unit

Title: Application of metagenomics in poultry research

Author
item Day, James

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: October 28, 2011
Publication Date: November 3, 2011
Citation: Day, J.M. 2011. Application of metagenomics in poultry research. Meeting Abstract. "Application of metagenomics in poultry research". 2011 Australian Veterinary Poultry Association Meeting. Melbourne, Australia. p.39-40.

Technical Abstract: The complicated microbiota in the gut of agriculturally important animals has a direct impact on animal health, fitness, and performance. The advent of high-throughput nucleic acid sequencing has allowed our laboratory to assemble a more complete—albeit more complicated—picture of the gut microbiota in poultry. The use of modern molecular techniques is essential to the identification and full characterization of novel enteric viruses that may play roles in the onset of enteric disease or in poultry production and performance problems in general, and can be accomplished without a priori knowledge of the viral population in question. The turkey gut ribonucleic acid (RNA) virus metagenome produced in our laboratory revealed viral sequences from the double-stranded RNA viruses (Reoviridae and Picobirnaviruses), and the single-stranded RNA viruses (Caliciviridae, Leviviridae, Picornavirales, and Astroviridae). The majority of the assigned viral contigs from the turkey gut showed similarity to database sequences from the Picornavirales order and other picorna-like viruses. A similar clone-based approach has revealed novel enteric turkey and chicken parvoviruses and a novel turkey microphage. Subsequent investigations in our laboratory have focused on comparative metagenomic analyses designed to identify enteric disease-associated viruses and genes. The present report will focus on the novel and unique poultry enteric viruses we have identified using this and similar approaches, and will provide details on the bioinformatic workflow developed to analyze the extensive sequence data generated during our comparative investigations.

Last Modified: 4/16/2014
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