Metabolomics in Biotechnology (Microbial Metabolomics)

Abstract

IntroductionThe first documentation of the term metabolomics goes back to two independent publications in 1998 and was used in the context of describing the metabolic behavior of microbial systems, showing a distinct phenotype regarding their physiology and extracellular metabolite spectrum [1,2]. For sure, these were not the first publications with such research activity, but these were the ones which obviously coined the term metabolomics. Later on, this term was picked up by the scientific community not only for the microbial field but also for many other scientific areas and paved its way to become one of the representatives of the omics era. In this sense, the suffix -ome is ''used to direct attention to holistic abstractions, an eventual goal, of which only a few parts may be initially in hand'' [3] and its origin goes back to the early twentieth century. Initially, the German botanist Hans Winkler is attributed to have coined the term genome by the combination of the terms gene and chromosome (Greek word soma = body) [4]. This keyword functioned as blueprint for the many other -omes that are currently investigated. Finally, they all go back to the Greek word soma and in opposite to the genome this term seems to be not precisely fitting for the metabolome, as the metabolites are not located or arranged in a body, but are distributed all over the system.Since 1998, the term metabolomics was increasingly used in the literature showing significant increase (Figure 15.1) and indicating the fast development of the field.The field of microbial metabolomics can be subdivided into the investigation of the endo-and exo-metabolome (intra-vs extracellular) as well as different approaches such as target analysis, metabolic profiling, and metabolic finger-/footprinting (Figure 15.2) [5,6]. On the one hand, the target analysis aims at the quantitative analysis of substrate and/or product metabolites of a given metabolic conversion, whereas metabolic profiling focuses on the quantitative analysis of a set of predefined metabolites belonging to a class of compounds or members of particular pathways or a linked group of metabolites (e.g., sugars, sugar phosphates, lipids, organic acids). On the other hand, metabolic Metabolomics in Practice: Successful Strategies to Generate and Analyze Metabolic Data, First Edition. Edited by Michael Lämmerhofer and Wolfram Weckwerth.

Continuous enzymatic stirred tank reactor cascade with unconventional medium yielding high concentrations of (S)-2-hydroxyphenyl propanone and its derivatives

“…A detailed analysis of real endogenous metabolite concentrations could be gained by instrumental analytics like MS-based metabolism methods. 37,38 Hence, 5 mM ThDP and 25 mM Mg 2+ were supplemented to the buffer, which was then added to the MARS system directly in the cSTR chamber. Notably, the possibility of cofactor leakage from the hydrophilic cell interior into the organic system was estimated to be low, as both cofactors are highly polar and are believed not to dissolve in the MTBE based substrate solution in high amounts.…”