Flux sampling in genome-scale metabolic modeling of microbial communities

Abstract

Abstract Background Microbial communities play a crucial role in ecosystem function through metabolic interactions. Genome-scale modeling is a promising method to understand these interactions and identify strategies to optimize the community. Flux balance analysis (FBA) is most often used to predict the flux through all reactions in a genome-scale model; however, the fluxes predicted by FBA depend on a user-defined cellular objective. Flux sampling is an alternative to FBA, as it provides the range of fluxes possible within a microbial community. Furthermore, flux sampling can capture additional heterogeneity across a population, especially when cells exhibit sub-maximal growth rates. Results In this study, we simulate the metabolism of microbial communities and compare the metabolic characteristics found with FBA and flux sampling. With sampling, we find significant differences in the predicted metabolism, including an increase in cooperative interactions and pathway-specific changes in predicted flux. Conclusions Our results suggest the importance of sampling-based approaches to evaluate metabolic interactions. Furthermore, we emphasize the utility of flux sampling in quantitatively studying interactions between cells and organisms.

Keywords

• Genome-scale metabolic modeling
• Microbial communities
• Flux sampling
• Cell metabolism