Jun 7, 2013

Community flux balance analysis for microbial consortia at balanced growth

PloS One
Ruchir A KhandelwalFrank J Bruggeman

Abstract

A central focus in studies of microbial communities is the elucidation of the relationships between genotype, phenotype, and dynamic community structure. Here, we present a new computational method called community flux balance analysis (cFBA) to study the metabolic behavior of microbial communities. cFBA integrates the comprehensive metabolic capacities of individual microorganisms in terms of (genome-scale) stoichiometric models of metabolism, and the metabolic interactions between species in the community and abiotic processes. In addition, cFBA considers constraints deriving from reaction stoichiometry, reaction thermodynamics, and the ecosystem. cFBA predicts for communities at balanced growth the maximal community growth rate, the required rates of metabolic reactions within and between microbes and the relative species abundances. In order to predict species abundances and metabolic activities at the optimal community growth rate, a nonlinear optimization problem needs to be solved. We outline the methodology of cFBA and illustrate the approach with two examples of microbial communities. These examples illustrate two useful applications of cFBA. Firstly, cFBA can be used to study how specific biochemical limitations in r...Continue Reading

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  • Citations55

Citations

Mentioned in this Paper

Microorganism
Metabolic Process, Cellular
Thermodynamics
In Silico
Extracellular
Metabolic Networks
Metabolic Networks and Pathways
Protoplasm
Competitive Behavior, Microbial
Uptake

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