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AbstractMetabolism encompasses the biochemical basis of life and as such spans all biological disciplines. Many decades of basic research, primarily in microbes, have resulted in extensive characterization of metabolic components and regulatory paradigms. With this basic knowledge in hand and the technologies currently available, it has become feasible to move toward an understanding of microbial metabolism as a system rather than as a collection of component parts. Insight into the system will be generated by continued efforts to rigorously define metabolic components combined with renewed efforts to discover components and connections using in vivo–driven approaches. On the tail of a detailed understanding of components and connections that comprise metabolism will come the ability to generate a comprehensive mathematical model that describes the system.

While microbes provide the logical organism for this work, the value of such a model would span biological disciplines. Described herein are approaches that can provide insight into metabolism and caveats of their use. The goal of this review is to emphasize that in silico, in vitro, and in vivo approaches must be used in combination to achieve a full understanding of microbial metabolism.

Figure 1 ( a) Shown is a diagram of the known biochemical pathways for thiamine biosynthesis in Salmonella enterica; key metabolites are depicted structurally. Gene products (when known) are listed under the step they catalyze. Abbreviations: AIR, aminoimidazole ribotide; HMP-PP, 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate; PRA, phosphoribosylamine; THZ-P, thiazole phosphate; TMP, thiamine monophosphate; DXP, deoxy-D-xylulose-5-phosphate. ( b) Diagram of thiamine model system used to probe metabolism. Represented are the multiple connected pathways in the model system.