The availability of whole-genome sequences has
opened up new technologies to study the behaviour of
microorganisms, the so-called ‘omics’ technologies [26].
While the genomes of microorganisms are rather static,
their transcriptomes and proteomes are highly dynamic
and subject to continuous change and adjustment in
response to the environment and phases of the cell cycle.
The use of DNA arrays and more recently RNA-seq technologies
make it possible to obtain snapshots of the gene
expression profile simultaneously in both pathogen and
host [27]. Similarly, two-dimensional gel electrophoresis
and multidimensional liquid chromatography, coupled to
mass spectrometry, facilitate a similar view of the protein
composition of the cell under different growth conditions
[28]. Such studies can be extended to study the concentrations
of metabolites (metabolomics) and the dynamic flux
of metabolites through the metabolic pathways (fluxomics)
[29]. Finally, next-generation sequencing has facilitated
the new field of metagenomics, with major studies
aimed at cataloguing the microbial flora of, for example,
the human gut, skin and oral cavity, with the aim of better
understanding the complex relationship between humans
and microbes [30].