Metabolomics can be applied to identify targets or bottlenecks for strain improvement and medium optimization in an unbiased manner. Recently, we have set-up a quantitative metabolomics platform that allows the analysis of ‘snapshot' metabolomes (1-3).

To demonstrate the merits of the metabolomics approach, we have studied phenylalanine production by Escherichia coli. An experimental design was defined that resulted in large differences in the phenylalanine titer when E. coli was cultivated under different defined environmental conditions. Samples were taken from these fermentations, quenched to halt cellular metabolism and subsequently analyzed by comprehensive GC-MS and LC-MS techniques. The metabolomics data was analyzed with the multivariate data analysis tool PLS, in order to rank the important metabolites. The data were biologically interpreted and a number of genetic targets were identified. Mutants were constructed by overexpression or deletion of these target-genes and tested on their phenylalanine production. This resulted in an increase in the phenylalanine yield of up to 50 %. These results demonstrated that the selection of targets for strain and medium improvement via the metabolomics-methodology is a valid approach.

1. Koek MM, et al. (2006) Anal Chem 78:1272

2. Couler L, et al. (2006) Anal Chem 78:6573

3. van der Werf MJ, et al. (2005) J Ind Microbiol Biotechnol 32:234