The increasing availability of complete genome sequences and advances in
analytical techniques for functional genomics make it possible to study microbial
metabolism from a global perspective. Prior to the genomics era,
metabolic studies were, of necessity, focused on individual or small numbers
of genes or enzymes involved in particular metabolic pathways and hence
were limited in providing useful information for analyzing global regulatory
networks governing bacterial metabolism. High-throughput analysis of all
messenger RNAs (transcriptome), proteins (proteome), and metabolites
(metabolome) provides microbiologists with a new set of tools with which to
investigate bacterial metabolism and integrate this knowledge at all levels of
cellular processes.
In this chapter, we begin with a brief description of traditional strategies for
studies of metabolism, including flux analysis, which is one of the earliest
global perspectives of microbial physiology. We then consider how the tools
of functional genomics, and in particular transcriptome analysis, have broadened
and will continue to broaden our understanding of metabolic networks.