Metabolomic diversity in the species Escherichia coli and its relationship to genetic population structure

The genomic richness and intra-species heterogeneity of the prokaryotic world is suggestive of extensive biochemical diversity. In this study, metabolomic profiling permitted a phylogenetic assessment of metabolic diversification amongst environmental, medical and laboratory strains of Escherichia coli. Strikingly, no two E. coli isolates exhibited the same metabolite pool profile. Only 27% of detected metabolite spots in 2-dimensional high-performance thin layer chromatography (2DHPTLC) were found in all strains, indicating that a relatively small core of metabolism is conserved across a species. The population structure determined using metabolomics exhibited clustering of strains in parallel to genetic relatedness, as established by multi-locus DNA sequencing. On the other hand, metabolome patterns did not cluster in parallel with the pathogenicity or environmental origins of strains, but some unique spots were found in most bacteria. These results suggest that great metabolic diversity, to the point of individuality, is likely to be characteristic of a bacterial species. Furthermore, the high resolving power of 2DHPTLC metabolite fingerprinting provides an economic and powerful means of using metabolomics for the analysis of evolutionary relationships and the precise typing of organisms.