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Nat Rev Microbiol. 2011 Jan;9(1):39-50. doi: 10.1038/nrmicro2456. Epub 2010 Dec 6.

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.

Author information

  • 1Department of Chemical Engineering and Applied Chemistry, and Institute of Biomaterials and Biomedical Engineering, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada.

Erratum in

  • Nat Rev Microbiol. 2011 Mar;9(3):222.


There is a wide diversity of unexplored metabolism encoded in the genomes of microorganisms that have an important environmental role. Genome-scale metabolic modelling enables the individual reactions that are encoded in annotated genomes to be organized into a coherent whole, which can then be used to predict metabolic fluxes that will optimize cell function under a range of conditions. In this Review, we summarize a series of studies in which genome-scale metabolic modelling of Geobacter spp. has resulted in an in-depth understanding of their central metabolism and ecology. A similar iterative modelling and experimental approach could accelerate elucidation of the physiology and ecology of other microorganisms inhabiting a diversity of environments, and could guide optimization of the practical applications of these species.

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