Fast sampling for quantitative microbial metabolomics

Targeted metabolomics, aimed at the study of metabolic reaction networks and their regulation in vivo, is a rapidly emerging field in systems biology. Obtaining proper quantitative snapshots of the microbial metabolome requires fast sampling, immediate quenching of enzymatic activity, separation of exometabolome and endometabolome, complete metabolite extraction from the cells, and reliable high-throughput analysis methods. This review addresses the current state of the art of rapid sampling and quenching for microbial metabolomics. Several robust and reliable rapid sampling devices have been developed. Various quenching and separation procedures have been proposed and applied, but with respect to the reliability of the different methods the literature is contradictory. To date a reliable universal method applicable to different microbial species is still lacking.