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USE OF COMPETITIVE GENOMIC HYBRIDIZATION TO ENRICH FOR GENOME-SPECIFIC DIFFERENCES BETWEEN TWO CLOSELY RELATED HUMAN FECAL INDICATOR BACTERIA
Citation:
SHANKS, O. C., J. SANTO DOMINGO, AND J. GRAHAM. USE OF COMPETITIVE GENOMIC HYBRIDIZATION TO ENRICH FOR GENOME-SPECIFIC DIFFERENCES BETWEEN TWO CLOSELY RELATED HUMAN FECAL INDICATOR BACTERIA. Presented at American Society for Microbiology Annual Meeting, Atlanta, GA, June 04 - 09, 2005.
Impact/Purpose:
To inform the public
Description:
Enterococci are frequently used as indicators of fecal pollution in surface waters. To accelerate the identification of Enterococcus faecalis-specific DNA sequences, we employed a comparative genomic strategy utilizing a positive selection process to compare E. faecalis and E. faecium genomes and enrich for E. faecalis genome-specific DNA sequences. Experiments yielded 300 probable genome-specific sequences. Genome specificity was confirmed for 225 DNA sequences with a comparative sequence analysis using BLAST and BLAT algorithms. E. faecalis genome-specific sequences ranged from genes encoding phage related proteins to putative surface-exposed proteins, and even detected short regions of variation embedded in highly conserved rrn sequences. This study confirms the use of comparative genomics to recognize DNA loci that may be used as indicators of fecal pollution and the potential to identify microorganism-specific genetic markers for stress responses, virulence, carbon utilization, and cell-to-cell communication pathways.