During the last few years, there have been enormous strides in the ability of microbiologists to analyse complete microbial genomes, the amount of information obtained from these sequences being quite astonishing, not least with respect to deciphering the role of microbial interactions within an environmental context. However, the measurement of metabolic changes could offer even deeper insights into biological mechanisms (as compared to simple DNA sequencing alone), by actually defining and interpreting the responses of microbial systems to environmental and/or genetic modifications. In this respect, (meta-) metabolomics is a recent discipline that attempts to study metabolites and their concentrations, interactions and dynamics at a global level within complex samples. It constitutes one of the tools of the post-genomic era, all of which are concerned with the study of the different functional levels of biological systems, i.e. the (meta-) transcriptome, the (meta-) proteome and the (meta-) metabolome.
The analysis of small metabolites is important because these molecules participate in the metabolic reactions necessary for the normal functioning, maintenance and growth of a cell. In this context, the primary goal of this chapter is to provide a general overview of the techniques, problems and prospects of microbial (meta-) metabolomics with respect to medical microbiological research and diagnosis. A key objective is to show how the fingerprinting analysis of intra- and extracellular metabolites can be used as a reflection of metabolic microbial activities that impact on microbial cell physiology, microbemicrobe interactions, microbe-host interactions, and on the analysis of whole microbial communities.