Ultrahigh resolution mass spectrometry based non-targeted microbial metabolomics

Microbial metabolomes gain more and more attention due to the fact that microorganisms are ubiquitous and important in environment and health. Some are involved in basic environmental processes and govern element cycles in the entire ecosystem; others have relevance for animals and human (as commensal or pathogens) and have the potential to be used in biotechnology. The tools of Metabolomics have been used for many years in microbial research and the paradigm is changing from studies on single species cultures to multispecies communities, like in biofilms or environmental and human microbiomes. These changes lead to a new variety of metabolomic tools (metametabolomics) adapted to the study of multiple organisms systems. In addition the needs in high-resolution instrumentation are changing to analytical platforms that enable to deal with the yet unknown compounds. ICR-FT/MS is a promising ultrahigh resolution mass spectrometry approach mastering the challenge in non-targeted metabolomics. This chapter presents an introduction to the current state of the art in microbial metabolomics, the importance of ICR-FT/MS in this field and is describing solutions for non-targeted metabolomics with a focus on bacterial samples.