ArticleApplied and environmental microbiology2006
Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples.
Article in Applied and environmental microbiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- QMRA for assessing treatment needs of surface water for drinking: trends and challenges in fecal pathogen quantification.Journal of water and health · 2025Review
- An overview of molecular markers for identification of non-human fecal pollution sources.Frontiers in microbiology · 2023Review
- A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border.Frontiers in microbiology · 2021Article
- Microbial Source Tracking of Fecal Indicating Bacteria in Coral Reef Waters, Recreational Waters, and Groundwater of Saipan by Real-Time Quantitative PCR.Frontiers in microbiology · 2020Article
- Extended persistence of general and cattle-associated fecal indicators in marine and freshwater environment.The Science of the total environment · 2019Article
- PCR data and comparative performance ofData in brief · 2018Article
- Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii.Applied and environmental microbiology · 2015Article
- Discovering new indicators of fecal pollution.Trends in microbiology · 2014Review
- Age-related shifts in the density and distribution of genetic marker water quality indicators in cow and calf feces.Applied and environmental microbiology · 2014Article
- Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters.Applied and environmental microbiology · 2012Article
- Genetic markers for rapid PCR-based identification of gull, Canada goose, duck, and chicken fecal contamination in water.Applied and environmental microbiology · 2012Article
- Hypothesis-driven approach for the identification of fecal pollution sources in water resources.Environmental science & technology · 2011Article
- Community structures of fecal bacteria in cattle from different animal feeding operations.Applied and environmental microbiology · 2011Article
- Presence of Bacteroidales as a predictor of pathogens in surface waters of the central California coast.Applied and environmental microbiology · 2010Article
- Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution.Applied and environmental microbiology · 2010Article
- Quantitative PCR for genetic markers of human fecal pollution.Applied and environmental microbiology · 2009Article
- Pig manure contamination marker selection based on the influence of biological treatment on the dominant fecal microbial groups.Applied and environmental microbiology · 2009Article
- Assessment of bias associated with incomplete extraction of microbial DNA from soil.Applied and environmental microbiology · 2009Article
- Temporal assessment of the impact of exposure to cow feces in two watersheds by multiple host-specific PCR assays.Applied and environmental microbiology · 2008Article
- Phylogenetic diversity and molecular detection of bacteria in gull feces.Applied and environmental microbiology · 2008Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine 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 bovine GFE sequences exhibited extremely high specificity (>99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by 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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