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Genomic Analyses Could Lead to “Field Guide to Microbes”

The swell of enthusiasm for analyzing microbial genomes continues, with keen interest in doing more and more genomes in smaller analytic formats at lower costs. Even while greater numbers of microbiologists jump into this fray, some continue to fret over what to make of these expanding findings, sharing thoughts and insights during several sessions, including the symposium "Microbial Single-Cell Genomics" and the colloquium "The $1 Bacterial Genome," convened during the 109th ASM General Meeting, held last May in Philadelphia, Pa.

"Single-cell genomics is a reality," says symposium participant Paul Blainey of Stanford University in Stanford, Calif. He described an approach that depends on microfluidic devices and other comparably scaled manipulative procedures for plucking single bacterial cells, including from human anatomic sites such as the skin and oral cavity, for genomic analysis. "You need 1 pg or less of DNA to carry out a sequencing run, even though manufacturers recommend samples containing 1,000 times more material," he says.

Microbial genomic sequencing is not merely driving miniaturization and other innovative technologydevelopment projects. It is also leading some experts in the field to ponder new means for collating and analyzing the volumes of sequencing data being produced, and also to identify which segments of the microbial world are underanalyzed and thus still poorly appreciated in the new genomicscentric scheme, according to colloquium participant Jonathan Eisen of the University of California, Davis, Genome Center.

For instance, a genomic encyclopedia project sponsored by the Department of Energy lays out which phyla include species whose genomic sequences are already analyzed, which are not, and which ones are "sparsely populated," Eisen points out. Such collections can provide a valuable "scaffold" for sorting genomic data and also for "annotating predicted functions," he says, suggesting such efforts could lead to a "field guide to microbiology."

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