Significance: Multiple Escherichia coli genome sequences have recently been made available by advances in DNA sequencing. Analysis of these genomes has demonstrated that the fraction of genes common to all E. coli strains in the species represents a small fraction of the entire E. coli gene pool. This observation raises the question: what is a strain and what is a species? In this study, genome-scale metabolic reconstructions of multiple E. coli strains are used to reconstruct the metabolic network for an entire species and its strain-specific variants. The models are used to determine functional differences between strains and define the E. coli species based on common metabolic capabilities. Individual strains were differentiated based on niche-specific growth capabilities.

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