Whole Genome Microarrays: Library on a Slide

A new application of microarray technology is being used to print up to 30,000 whole genomes on a single slide, which is designed to help researchers compare the genetic make-up of large numbers of bacterial strains to discover which genes are responsible for causing disease. The new application was reported in the March 21, 2004, issue of the online journal BMC Microbiology (Biomed Central).

Genetic content can vary by as much as 25% between individual strains of bacteria even within one species. These differences can determine how virulent a particular strain is or which organisms it can colonize. To make claims about which genes play a role in which biologic processes, researchers have to compare large numbers of bacterial genomes and find which genes are associated with a particular trait.

To make this work easier, the "library on a slide” was developed, based on current microarray technology. The printing and probing of the slide are much the same, except that each spot on the slide contains the genomic DNA of one bacterial strain rather than containing multiple copies of a single gene.

To test the method, researchers created a sample array using a collection of Escherichia coli genomes, and probed these to discover which genomes contained the hemolysin gene, a known virulence factor. The results from the array experiment matched perfectly with results from experiments using dot blot and Southern hybridization methods.

The experiment was led by Dr. Lixin Zhang and colleagues from the University of Michigan (Ann Arbor, MI, USA), who predict their method will be "an efficient and cost-effective way for sharing and utilizing large strain collections in various comparative genomics studies.”