DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes

DNA microarrays constructed with full length ORFs from Shewanella oneidensi s, MR-1, were hybridized with genomic DNA from nine other Shewanella specie s and Escherichia coli K-12. This approach enabled visualization of relatio nships between organisms by comparing individual ORF hybridizations to 164 genes and is further amenable to high-density high-throughput analyses of c omplete microbial genomes. Conserved genes (arcA and ATP synthase) were ide ntified among all species investigated. The mtr operon, which is involved i n iron reduction, was poorly conserved among other known metal-reducing She wanella species. Results were most informative for closely related organism s with small subunit rRNA sequence similarities greater than 93% and gyrB s equence similarities greater than 80%. At this level of relatedness, the si milarity between hybridization profiles was strongly correlated with sequen ce divergence in the gyrB gene. Results revealed that two strains of S. one idensis (MR-1 and DLM17) were nearly identical, with only 3% of the ORFs hy bridizing poorly, in contrast to hybridizations with Shewanella putrefacien s, formerly considered to be the same species as MR-1, in which 63% of the ORFs hybridized poorly (log ratios below -0.75). Genomic hybridizations sho wed that genes in operons had consistent levels of hybridization across an operon in comparison to a randomly sampled data set, suggesting that simila r applications will be informative for identification of horizontally acqui red genes. The full value of microbial genomic hybridizations lies in provi ding the ability to understand and display specific differences between clo sely related organisms providing a window into understanding microheterogen eity, bacterial speciation, and taxonomic relationships.