‘Library on a Slide’: whole genome microarrays for comparative genomics

A novel application of microarray technology, where up to 30,000 whole genomes are printed on a single slide, is described in the journal BMC Microbiology this week. The ‘Library on a Slide’ will help researchers compare the genetic make up of large numbers of bacterial strains to discover which genes are responsible for causing disease.

Even within one species of bacteria, the genetic content can vary by as much as 25% between individual strains. These differences can determine how virulent a particular strain is or which organisms it can colonise. To make significant claims about which genes play a role in which biological processes, researchers must compare large numbers of bacterial genomes and see which genes are associated with a particular trait.

Dr Lixin Zhang and his colleagues from University of Michigan have made this sort of experiment much easier, by developing the ‘Library on a Slide’ technique. They predict that their high-throughput method will be, “an efficient and cost effective way for sharing and utilizing large strain collections in various comparative genomics studies.”

The ‘Library on a Slide’ is based on current microarray technology – the printing and probing of the slide are carried out largely as usual. The most significant difference is that each spot on the slide contains the genomic DNA of one bacterial strain, rather than containing multiple copies of a single gene.

The researchers describe how they adapted a high-throughput method for isolating small DNA fragments to efficiently isolate high quality genomic DNA, and how they optimized the conditions for printing this genomic DNA at high density onto a glass slide. They also tested techniques for identifying individual target genes at high sensitivity using fluorescently labelled probes.

To test the ‘Library on a Slide’ method the group created a sample array using a collection of E. coli genomes, and probed this 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 hybridisation methods.

The researchers can envisage other ways that their technique could develop:

“A single ‘Library on a Slide’ could also be constructed with isolates from several related species, or species that are part of a microbial ecosystem. Such a platform would enable us to examine the extent of shared genetic elements across species – especially horizontally transferred virulence factors and antibiotic resistance genes.”