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More Microbial Genomes at ASM

The second full day of the American Society for Microbiology annual meeting was chock-full of 'omics-related research.

In a Monday morning plenary on interrogating microbial genomes, Christopher Lee from the University of California, Los Angeles, described a phenotype sequencing approach to screen multiple independent microbial mutants using high-throughput sequencing. Using a two-fold pooling library prep and sequencing approach as well as his group's Phenoseq package is a cost-effective method to efficiently identify the cause of a particular mutant phenotype, Lee said.

During that same session, the University of California, San Francisco's Carol Gross discussed her group's efforts to build upon high-throughput interaction profiling studies in yeast, extending their application to bacteria. Such profiling studies can provide mechanistic insights into cellular processes, she said. Gross added it is important to "make more efficient use of the model organisms we study and bootstrap that into our studies of other organisms." Gross presented her and her colleagues' chemical genomics profiling study of 4,000 E. coli mutants across 120 different stress conditions through which they created a comprehensive interaction profile and found that orphan genes are well-represented, though narrowly distributed. In her talk, Gross called this approach a "pathway for discovery of orphan [gene] functions," and said that "many orphan genes correlate strongly to annotated genes."

Pacific BioSciences' Eric Schadt spoke during Monday's ASM President's Forum about whole-genome sequencing for pathogen surveillance. Schadt, who also directs the Institute for Genomics and Multiscale Biology at the Mount Sinai School of Medicine in New York, discussed how his group has re-analyzed the genomic data for the 2011 German E. coli outbreak strain it produced using PacBio's SMRT (which was published in the New England Journal of Medicine last August). This time, he and his team considered kinetic information and how that might relate to epigenetic modifications. Compared with highly related strains, the researchers found a methyltransferase in the outbreak strain that targets CTGCAG motifs, leading those genes to be upregulated two-fold, Schadt said.

During an afternoon symposium covering best practices for rapid and emerging diagnostic techniques, James Musser from the Methodist Hospital Research Institute in Houston, Texas, discussed bacterial genome sequencing in the clinic. Musser noted that, at present, clinical microbiology labs and genome research centers tend to operate as geographically and culturally distinct entities. "Destruction of these differences is critical," he said. In order to fully integrate genomics into the clinical lab, both geographic and cultural walls must be broken down, Musser stressed.

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