Using DNA microarrays to identify library-independent markers for bacterial source tracking

Applied and Environmental Microbiology
Marilyn SouleD R Call

Abstract

Bacterial source tracking is used to apportion fecal pollution among putative sources. Within this context, library-independent markers are genetic or phenotypic traits that can be used to identify the host origin without a need for library-dependent classification functions. The objective of this project was to use mixed-genome Enterococcus microarrays to identify library-independent markers. Separate shotgun libraries were prepared for five host groups (cow, dog, elk/deer, human, and waterfowl), using genomic DNAs (gDNAs) from ca. 50 Enterococcus isolates for each library. Microarrays were constructed (864 probes per library), and 385 comparative genomic hybridizations were used to identify putative markers. PCR assays were used to screen 95 markers against gDNAs from isolates from known sources collected throughout the United States. This validation process narrowed the selection to 15 markers, with 7 having no recognized homologues and the remaining markers being related to genes involved in metabolic pathways and DNA replication. In most cases, each marker was exclusive to one of four Enterococcus species (Enterococcus casseliflavus, E. faecalis, E. hirae, or E. mundtii). Eight markers were highly specific to either cattle...Continue Reading

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Citations

Jan 7, 2011·Applied Microbiology and Biotechnology·Peter Roslev, Annette S Bukh
Jul 27, 2011·Environmental Science & Technology·Yiping CaoPatricia A Holden
Jan 9, 2007·Applied and Environmental Microbiology·Yan WanDouglas R Call
Jun 6, 2006·Applied and Environmental Microbiology·Matthew J HamiltonMichael J Sadowsky
Dec 4, 2012·Microbiology and Molecular Biology Reviews : MMBR·Muruleedhara N ByappanahalliValerie J Harwood
Apr 2, 2013·Canadian Journal of Microbiology·Corinne A KrentzJudith Isaac-Renton
Aug 6, 2008·BMC Bioinformatics·Da MengDouglas R Call
Jan 1, 2008·Microbes and Environments·Satoshi Ishii, Michael J Sadowsky
Jul 24, 2007·Water Research·Katharine G Field, Mansour Samadpour
Mar 15, 2015·Applied and Environmental Microbiology·Sheridan K HaackWilliam T Foreman
Feb 21, 2008·Environmental Science & Technology·Mark D LeachDouglas R Call
Apr 19, 2007·Environmental Science & Technology·Satoshi IshiiMichael J Sadowsky

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