A rapid sampling and the following sample processing are the critical phases in microbial metabolomics. Due to the complicated procedures and the high quantity of parameters there are many possibilities for variations and errors. The effective and sufficient separation of the exo- and endometabolome is a specific challenge in this context. Our aim is to find new technologies and methods to minimize the absolute error and to design new experiments to investigate and describe the metabolism.

Rapid Sampling Unit
A new fully automated rapid sampling unit is under development. The concept combines flexibility and accuracy. The rapid sampling unit is based on a modular system. A specific valve system assures definite sample volumes and efficient mixing of the sample with the quenching solution. Upon completion the system should be able to handle five hundred samples with a frequency up to ten samples per second. All parts with contact to the fermentation broth are in situ sterilizable to permit the work with pathogenic organisms. Due to the modular construction several experimental setups are possible. For example different quenching methods could be tested or the dynamic behavior of the metabolism after a change in the culture conditions could be observed. For development a 3D model of the rapid sampling unit has been generated, which allows easy design of new components for new experiments.

Sample processing
In focus of our research are also different quenching and extraction methods to establish a protocol with high accuracy for the separation of intra- and extracellular metabolites. All steps of the sample processing are evaluated and new technologies are tested.