The Coming Revolution: Microbes and Multiscale Biology
Eric E. Schadt
2013
Microbe Magazine
New technologies are providing a more complete view of the functional dynamics of microorganisms such as E. coli and V. cholerae Eric E. Schadt Microbes continue to be at the cutting edge of research-particularly in the arena of multiscale biology, where many dimensions of data are combined to form fuller and more dynamic pictures of specifıc microorganisms. Where we once relied on Southern blots to examine single genes, we can now characterize the full complement of DNA, RNA, and many
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... c markers at a genome-wide scale in a matter of hours. A few recent microbial projects highlight the tremendous power of current technologies to elucidate biological systems at a level that was not possible, such as the genome-wide characterization of a broad range of chemical modifıcations to DNA bases. These studies offer a glimpse of where such analyses may take us during the next few years. How a Cholera Strain Reached Haiti Late in 2010, tens of thousands of Haitians succumbed to a severe strain of cholera after a dev-astating earthquake that left whole swaths of the population living in unsanitary conditions. Within about six months, more than 4,500 individuals died from this epidemic. Amid the epidemic, a controversy arose as to the source of the cholera. A United Nations peacekeeping group from Nepal was one possible source of the strain, which others said was endemic in contaminated untreated waters that displaced populations were drinking (Microbe, December 2011, p. 522). To resolve this question, Matthew Waldor of Harvard Medical School in Boston, Mass., collected several samples of the Vibrio cholerae strain circulating in Haiti and sent them to me and my colleagues at Pacifıc Biosciences to analyze. Along with two samples from the Haitian outbreak, we sequenced DNA from three V. cholerae clinical isolates from Latin America and Bangladesh, and compared them to reference genomes. We then analyzed single nucleotide and copy number variations to determine the likely phylogeny of the Haitian strain. According to our analysis, it is closely related to recent strains from southern Asia that also cluster tightly with two isolates from recent outbreaks in Bangladesh, as noted in our report in the January 6, 2011 New England Journal of Medicine. The isolates from Haiti are more distantly related to strains from east Africa and Latin America, making it unlikely that the strain circulating in Haiti had been dormant there prior to the epidemic. Our results were confırmed by a number of other research groups, several of whom generated additional data on V. cholerae strains associated with more recent outbreaks in Latin America, Nepal, Africa, and other regions of interest. Because our data suggest that the Haitian epidemic began when a V. cholerae strain was intro-SUMMARY ➤ In multiscale biology, many dimensions of data are combined to form fuller and more dynamic pictures of specific microorganisms.
doi:10.1128/microbe.8.70.1
fatcat:6cadc7dembh5vf5xebamniwt2u