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COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES
Citation:
SHANKS, O. C., J. SANTO-DOMINGO, R. LAMENDELLA, C. A. KELTY, AND J. E. GRAHAM. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES. L. N. Ornston (ed.), APPLIED AND ENVIRONMENTAL MICROBIOLOGY. American Society for Microbiology, Washington, DC, 72(6):4054-4060, (2006).
Impact/Purpose:
to present information
Description:
Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, cattle fecal DNA was challenged against a pig fecal DNA background to select for cattle specific DNA sequences. Bioinformatic analyses of 380 cattle enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select Bacteroidales-like cattle GFE sequences exhibited extremely high specificity (> 99%) in PCR assays with total fecal DNA from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different cattle sources. These data demonstrate that direct metagenomic DNA analysis using the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers, and for characterizing differences between environmental microbial communities.
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COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES