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

s ago, but the plummeting cost of gene sequencing has made a plethora of other E. coli genomes available to compare with this first "model" strain. The wealth of genome data, Palsson said, has led some researchers to wonder whether the model organism fully represents the E. coli species.

In the PNAS study, Palsson and colleagues identified a core metabolic network shared by all the strains, as well as all the differences in metabolic content among the strains. Most of these differences appear to be in the ability to break down various nutrients, said Adam Feist, a project scientist in the UC San Diego Jacobs School of Engineering, alumnus of the Palsson lab in the bioengineering department, and the other corresponding author on the paper.

In retrospect, this variety isn't too surprising, he said, given the number of "diverse environmentson the skin, inside the body, outside in the dirt that E. coli are found in."

In future studies, Feist said, the researchers hope to "drill deeper" into this variation and explore whether strains that contain the same metabolic content "use that similar content differently."

The researchers found that their models could also identify E. coli strains that lack the genes to help them manufacture certain essential compounds, such as niacin. This phenomenon, called auxotrophy, often goes hand in hand with virulence. Many experiments have shown that when these missing genes are restored, the bacteria become less virulent. "So finding out why these strains have become auxotrophs could shed a lot of light on how an organism becomes a pathogen," Monk said.

The predictive success of the metabolic models has the team thinking about applying the method to other bacteria such as Staphylococcus aureus, said Palsson. "We intend to move aggressively forward with categorizing many human pathogens in this way."


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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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