Researchers Find Pathogens in Unlikely Places Using High-density Microarrays
February 2006
Scientists at Lawrence Berkeley National Laboratory and Defence Science and Technology Laboratory have developed a technique for identifying up to 3,200 organisms at once-in less than nine hours. The speed of this technique far outpaces serial cloning, and may be useful for numerous applications including bioterror agent detection and disease tracking. The researchers are using a smallsubunit (SSU) microarray to quickly classify and quantify eukaryotic and prokaryotic organisms in environmental samples.
It's known that microarrays can be used to quantify microbial genes. The real challenge for scientists lay in being able to classify and quantify a wide variety of microbial genes from both eukaryotes and prokaryotes-rapidly, and simultaneously. As reported in the March 23, 2005 online issue of the Federation of European Microbiological Societies (FEMS) Microbiology Letters, Dr. Gary Andersen and his colleagues have met this challenge using a custom SSU microarray from Affymetrix.
The SSU microarray is comprised of over 60,000 probes complementary to 16S rRNA-small ribosomal subunit sequences. The array includes probes for all 91 known prokaryotic orders and 14 eukaryotic phyla (or equivalent taxa), and a Perfect Match/Mismatch strategy was used to control for non-specific hybridization.
The research team believes they may be the first to simultaneously identify and quantify multiple rRNA gene types from a wide range of phylogenetic orders against an environmental background. This represents an important step towards high-throughput monitoring of microbes. The scientists also explored the effects of different DNA extraction protocols on resulting microbial diversity, finding significant reproducible differences. These findings will be useful in developing and optimizing protocols for future studies.
Dr. Gary Andersen continues to work with microarrays for pathogen detection, and shares his thoughts with the Affymetrix Microarray Bulletin (AMB) in the January 2006 issue.
