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Identification of chicken-specific fecal microbial sequences using a metagenomic approach.pdf

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Identification of chicken-specific fecal microbial sequences using a metagenomic approach

United States Environmental Protection Agency U.S. Environmental Protection Agency Papers University of Nebraska - Lincoln Year ???? Identification of chicken-specific fecal microbial sequences using a metagenomic approach Jingrang Lu? Jorge Santo Domingo? Orin Shanks? ?US Environmental Protection Agency ?US Environmental Protection Agency ?US Environmental Protection Agency This paper is posted at DigitalCommons@University of Nebraska - Lincoln. /usepapapers/18 Available at journal homepage: /locate/watres Identification of chicken-specific fecal microbial sequences using a metagenomic approach Jingrang Lu, Jorge Santo Domingo, Orin C. Shanks US Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, MS-387, Cincinnati, OH, USA a r t i c l e i n f o Article history: Received 20 February 2007 Received in revised form 7 May 2007 Accepted 15 May 2007 Available online 24 May 2007 Keywords: Chicken fecal DNA Competitive genomic hybridization Genetic markers Fecal microbial community a b s t r a c t In this study, we applied a genome fragment enrichment (GFE) method to select for genomic regions that differ among different fecal metagenomes. Competitive DNA hybridizations were performed between chicken fecal DNA and pig fecal DNA (CP) and between chicken fecal DNA and an avian DNA composite consisting of turkey, goose, and seagull fecal DNA extracts (CB) to enrich for chicken-specific DNA fragments. A total of 471 non-redundant chicken metagenomic sequences were retrieved and analyzed. All of the clone sequences were similar to prokaryotic genes, of which more than 60% could not be assigned to previously characterized functional roles. In general terms, sequences assigned characterized functional roles were associated with cellular processes (11.7%), metabolism (11.0%) and information storage and processing (13.4%). Approximately 53% of the non- redundant sequences are similar