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.
Keywords: Metabolomics, (Meta-) Metabolomics, Metabolomic Footprinting, Mass Spectroscopy, Nuclear
Magnetic Resonance, Microbiome, Metabolite Extraction.
