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New models predict where E. coli strains will thrive
Date:11/18/2013

Bioengineers at the University of California, San Diego have used the genomic sequences of 55 E. coli strains to reconstruct the metabolic repertoire for each strain. Surprisingly, these reconstructions do an excellent job of predicting the kind of environment where each strain will thrive, the researchers found.

Their analysis, published in the Nov. 18, 2013 early edition of the Proceedings of the National Academy of Sciences, could prove useful in developing ways to control deadly E. coli infections and to learn more about how certain strains of the bacteria become virulent.

And when "nasty new versions" of E. coli appear, the metabolic models may someday help researchers quickly identify and characterize these new strains, said Bernhard Palsson, professor of bioengineering at UC San Diego Jacobs School of Engineering and a corresponding author on the paper.

The reconstructions map out all the genes, reactions and products of metabolism for each strain and allow the researchers to probe their coordinated functionality. Each strain's metabolic capabilities, the researchers discovered, correspond to specific environmental niches. Commensal or "friendly" E. coli strains also can be distinguished from pathogenic strains using this technique.

"This paper shows that you can predict the microenvironmental niche where human pathogenic strains of E. coli grow, whether it's in your bladder or your stomach, or your blood or elsewhere, based on these sequences," Palsson said.

Jonathan Monk, a nanoengineering graduate student in the Jacobs School of Engineering and lead author of the paper, said that the metabolic reconstructions might also help researchers figure out ways to deprive pathogenic E. coli of the nutrients they need, "so that you can prevent them from getting an advantage in that niche, and maybe better control an infection that way."

The first E. coli strain was sequenced 15 year
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Contact: Daniel Kane
dbkkane@eng.ucsd.edu
858-534-3262
University of California - San Diego
Source:Eurekalert

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