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Nat Rev Microbiol. 2012 Feb 27;10(4):291-305. doi: 10.1038/nrmicro2737.

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

Author information

1
Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, USA.

Abstract

Reconstructed microbial metabolic networks facilitate a mechanistic description of the genotype-phenotype relationship through the deployment of constraint-based reconstruction and analysis (COBRA) methods. As reconstructed networks leverage genomic data for insight and phenotype prediction, the development of COBRA methods has accelerated following the advent of whole-genome sequencing. Here, we describe a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods. These methods have enabled genome-scale analysis of microbial metabolism for numerous basic and applied uses, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour.

PMID:
22367118
PMCID:
PMC3536058
DOI:
10.1038/nrmicro2737
[Indexed for MEDLINE]
Free PMC Article

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