Henson Michael A, Hanly Timothy J
Department of Chemical Engineering, University of Massachusetts, Amherst, MA 01007, USA.
IET Syst Biol. 2014 Oct;8(5):214-29. doi: 10.1049/iet-syb.2013.0021.
Dynamic flux balance analysis (DFBA) is an extension of classical flux balance analysis that allows the dynamic effects of the extracellular environment on microbial metabolism to be predicted and optimised. Recently this computational framework has been extended to microbial communities for which the individual species are known and genome-scale metabolic reconstructions are available. In this review, the authors provide an overview of the emerging DFBA approach with a focus on two case studies involving the conversion of mixed hexose/pentose sugar mixtures by synthetic microbial co-culture systems. These case studies illustrate the key requirements of the DFBA approach, including the incorporation of individual species metabolic reconstructions, formulation of extracellular mass balances, identification of substrate uptake kinetics, numerical solution of the coupled linear program/differential equations and model adaptation for common, suboptimal growth conditions and identified species interactions. The review concludes with a summary of progress to date and possible directions for future research.
动态通量平衡分析（DFBA）是经典通量平衡分析的扩展，它能够预测和优化细胞外环境对微生物代谢的动态影响。最近，这个计算框架已扩展到已知个体物种且可获得基因组规模代谢重建的微生物群落。在这篇综述中，作者概述了新兴的DFBA方法，重点介绍了两个案例研究，涉及合成微生物共培养系统对混合己糖/戊糖混合物的转化。这些案例研究阐述了DFBA方法的关键要求，包括纳入个体物种代谢重建、制定细胞外质量平衡、确定底物摄取动力学、耦合线性规划/微分方程的数值解以及针对常见的次优生长条件和已确定的物种相互作用进行模型适配。综述最后总结了迄今为止的进展以及未来研究可能的方向。
