Stoichiometric modelling of microbial metabolism

Methods Mol Biol. 2014;1191:3-18. doi: 10.1007/978-1-4939-1170-7_1.

Abstract

Stoichiometric models describe cellular biochemistry with systems of linear equations. The models which are fundamentally based on the steady-state assumption are comparatively easy to construct and can be applied to networks up to genome scale. Fluxes are inherent variables in stoichiometric models and linear optimization can be used to identify intracellular flux distributions. Great caution, however, has to be paid to the selection of the specific objective function which inevitably implies the existence of a specific global cellular rationale. On the other hand, stoichiometric models provide an analytical platform for contextualization of experimental data. Equally important, the stoichiometric models can be used for structural analyses of metabolic networks as such supporting for example rational model-driven strategies in metabolic engineering.

MeSH terms

  • Algorithms*
  • Metabolic Engineering / methods*
  • Metabolic Flux Analysis / methods*
  • Metabolic Networks and Pathways / physiology*
  • Microbiological Phenomena*
  • Models, Biological*
  • Models, Chemical*