Toward metabolic phenomics: Analysis of genomic data using flux balances

Small genome sequencing and annotations are leading to the definition of me tabolic genotypes in an increasing number of organisms. Proteomics is begin ning to give insights into the use of the metabolic genotype under given gr owth conditions. These data sets give the basis for systemically studying t he genotype-phenotype relationship. Methods of systems science need to be e mployed to analyze, interpret, and predict this complex relationship. These endeavors will lead to the development of a new field, tentatively named p henomics. This article illustrates how the metabolic characteristics of ann otated small genomes can be analyzed using flux balance analysis (FBA). A g eneral algorithm for the formulation of in silico metabolic genotypes is de scribed. Illustrative analyses of the in silico Escherichia coli K-12 metab olic genotypes are used to show how FBA can be used to study the capabiliti es of this strain.