Model based prediction of physiology of G. sulfurreducens by flux balance and thermodynamics based metabolic flux analysis approaches

The development of genome scale metabolic models have been aided by the increasing availability of genome sequences of microorganisms such as Geobacter sulfurreducens, involved in environmentally relevant processes such as the in-situ bioremediation of U(VI). Since microbial activities are the major driving forces for geochemical changes in the sub-surface, understanding of microbial behavior under a given set of conditions can help predict the likely outcome of potential subsurface bioremediation strategies. Hence, a model based lookup table was created to capture the variation in physiology of G. sulfurreducens in response to environmental perturbations. Thermodynamically feasible flux distributions were generated by incorporating thermodynamic constraints in the model. These constraints together with the mass balance constraints formed the thermodynamics based metabolic flux analysis model (TMFA). Metabolomics experiments were performed to determine the concentration of intracellular metabolites. These concentrations were posed as constraints in the TMFA model to improve the model accuracy.