March 18, 2013  |  Microbial sequencing methods

Sequencing Innovations Offer a More Complete Picture for Microbes

We’re pleased to share with you a recent article from Microbe magazine, a publication of the
American Society for Microbiology, from Eric Schadt, founding director of the
Icahn Institute for Genomics and Multiscale Biology at Mount Sinai School of
Medicine. Entitled “The Coming Revolution: Microbes and Multiscale Biology,” the article describes recent microbial
studies Schadt participated in, including analyses of the cholera strain in the
2010 Haiti outbreak and the E. coli
strain in the 2011 Germany outbreak.

Schadt writes about the tremendous technological strides
that have advanced the microbial research world: “Where we once relied on
Southern blots to examine single genes, we can now characterize the full
complement of DNA, RNA, and many epigenetic markers at a genome-wide scale in a
matter of hours.”

In the article, Schadt uses the cholera and E. coli projects as examples of these
advances. The scientists used single molecule, real-time (SMRT®)
sequencing of the cholera strain in Haiti to determine the phylogeny of the
strain, helping to resolve growing controversy over the origins of the
outbreak. Separately, using long-read sequencing for the E. coli strain enabled scientists to see changes that other teams
had missed with short-read sequence data, and corrected a misconception about
the serotype of the outbreak strain. They were also able to analyze genome-wide
methylation patterns to provide additional insight into the unusual virulence
of the microbe.
Schadt predicts that these cutting-edge tools and newfound
abilities to elucidate microbial biology will allow scientists to be more
holistic in their studies. “These tools enable us to appreciate the
complexities of microorganisms, in which networks of pathways and genes
interact to produce dynamic and intricate systems,” he writes. “The microbes
living in and around us are affecting us on a much deeper level than we
previously appreciated.”
For more on using PacBio® sequencing to study microbes,
don’t miss the ASM 2013 pre-conference workshop, “Studying Whole-Genome
Microbial Epigenetics.” It will be held on May 18 from 1:00 to 4:30, and
pre-registration is required through the ASM website. More details are available here.

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