The E. coli metabolic reconstruction and its GEM are highly developed. There are now a number of other microorganisms for which GEMs have been built and put to use. A significant feature of microbial life and biology revolves around metabolism and growth, and thus GEMs of microbial metabolism have been used to address a number of important issues in industrial, environmental, and medical microbiology. We will describe some of these accomplishments in this chapter. It is likely that the number of such reconstructions and their applications will grow significantly over the coming years given the rapidly growing amount of sequenced genomes and semi-automated reconstruction tools.

State of The Field

Phylogenetic coverage Bacteria display an astonishing spectrum of metabolic capabilities that reflect the wide spectrum of microenvironmental niches in which they grow. Metabolism in some of the branches of the phylogenetic tree, such as enterobacteria, is generally well characterized, whereas little molecular detail is known about members of other branches. In fact, a large number of microorganisms cannot even be cultured in the laboratory, but their genomes can be sequenced and a metabolic reconstruction can be performed. Interestingly, metabolic network reconstructions can then be used to formulate growth media [441].

The phylogenetic coverage of existing genome-scale metabolic reconstructions is shown in Figure 5.1A. It shows that the coverage of the tree is biased by well-understood model species. There is clearly a need to get better uniform coverage of the phylogenetic tree so that we can have a broad view of the metabolic capabilities of microbes that inhabit the various microenvironments on this planet.

The number of manually curated reconstructions has grown steadily since the publication of the first GEM in 1999 (Figure 5.1B). The iterative nature of the process also shows up in this summary, as metabolic reconstructions for some organisms have gone through multiple iterations (see Figure 3.11 for more details).