Anyone who has watched one of the CSI: Crime Scene Investigation television shows knows that PCR (Polymerase Chain Reaction) is a technology used to amplify the tiniest samples of DNA into forensic evidence that can identify perpetrators or victims of a crime. Microbiologists also use PCR to uncover the identity of microbes in samples taken from a wide range of sources for a wide range of purposes. However, for microbial analysis, the use of PCR technology can pose problems. Now, researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab) have overcome those problems with the development of PCR-free technology that is based on Berkeley Lab's award-winning, high-density DNA-based microarray known as the PhyloChip.
"We've developed two methods of PCR-independent microbial community analysis using the PhyloChip," says Gary Andersen, a microbial ecologist with Berkeley Lab's Earth Sciences Division. "Each method represents a simple and economical way to directly query microbial communities in natural environments and each offers the additional advantage of detecting the most metabolically active microbes in a community, the ones most likely to attenuate toxins, drive biogeochemical cycles or proliferate in disease states."
Andersen is the corresponding author of a paper published in the journal Applied and Environmental Microbiology that discusses this research. The paper is titled "PCR amplification-independent methods for detection of microbial communities by the high density microarray PhyloChip." Co-authoring the paper were Kristen DeAngelis, Cindy Wu, Harry Beller, Eoin Brodie, Romy Chakraborty, Todd DeSantis, Julian Fortney, Terry Hazen, Shariff Osman, Mary Singer and Lauren Tom.
How omnipresent are microbes in the environment? Extract a gram of soil from just about anywhere and you can expect to find many millions of individual microbes representing more than a thousand differe
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DOE/Lawrence Berkeley National Laboratory