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Using DNA microarrays to identify library-independent markers for bacterial source tracking
Marilyn Soule1, Edward Kuhn, Frank Loge
1Department of Microbiology and Pathology, Washington State University, 402 Bustad Hall, Pullman, WA 99164-7040, USA.
Applied and Environmental Microbiology
|March 7, 2006
Summary
This study developed library-independent markers for bacterial source tracking using Enterococcus microarrays. Researchers identified 15 specific genetic markers to trace fecal pollution origins from various hosts, improving water quality analysis.
Area of Science:
- Environmental microbiology
- Molecular biology
- Genomics
Background:
- Bacterial source tracking (BST) is crucial for identifying fecal pollution sources.
- Library-independent markers offer a method for host origin identification without prior classification.
- Enterococcus species are common indicators of fecal contamination.
Purpose of the Study:
- To identify novel library-independent markers for bacterial source tracking.
- To utilize mixed-genome Enterococcus microarrays for marker discovery.
- To validate potential markers for accurate host attribution.
Main Methods:
- Preparation of shotgun libraries from Enterococcus isolates of five host groups (cow, dog, elk/deer, human, waterfowl).
- Construction of microarrays (864 probes/library) and comparative genomic hybridizations (385 total).
- Screening of 95 putative markers using PCR assays on isolates from known US sources.
Main Results:
- Identification of 15 validated library-independent markers, 7 with no known homologues.
- Markers were often specific to Enterococcus species (E. casseliflavus, E. faecalis, E. hirae, E. mundtii).
- Eight markers showed high specificity for cattle, humans, or elk/deer; others indicated mixed host origins.
Conclusions:
- Developed and validated library-independent markers for Enterococcus-based BST.
- Markers demonstrate potential for differentiating fecal pollution sources.
- Prevalence variations and potential interpretation challenges of markers were noted.
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