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IDENTIFICATION OF CHICKEN-SPECIFIC FECAL MICROBIAL SEQUENCES USING A METAGENOMIC APPROACH
LU, J., J. W. SANTO-DOMINGO, AND O. C. SHANKS. IDENTIFICATION OF CHICKEN-SPECIFIC FECAL MICROBIAL SEQUENCES USING A METAGENOMIC APPROACH. WATER RESEARCH. Elsevier BV, AMSTERDAM, Netherlands, 41(16):3561-3574, (2007).
In this study, we applied a genome fragment enrichment (GFE) method to select for genomic regions that differ between different fecal metagenomes. Competitive DNA hybridizations were performed between chicken fecal DNA and pig fecal DNA (C-P) and between chicken fecal DNA and an avian DNA composite consisting of turkey, goose and seagull fecal DNA extracts (C-B) to enrich for chicken specific DNA fragments. Four hundred and seventy one 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%). Most of the non-redundant sequences are similar to genes present in intestinal bacteria belonging to Clostridia, Bacteroidetes and Bacilli. Twenty five sequences from the C-P and C-B clone libraries were selected to develop chicken fecal specific PCR assays. These assays were challenged against fecal DNA extracted from 21 different animal species, including mammals and birds. The results showed that 12 of the assays had a high degree of specificity to chicken feces. Three assays were specific to chicken and turkey and four assays tested positive to more than two avian species, suggesting a broader distribution of some of the enriched gene fragments among different avian fecal microbial communities. Fecal pollution signals were detected in contaminated water samples although the assays showed different levels of sensitivity. These results indicate the need for multiple assays to detect poultry fecal sources of pollution. The competitive DNA hybridization approach used in this study can rapidly select for numerous chicken fecal metagenomic regions that can be used as potential genetic markers for fecal source tracking.