Constraint-based stoichiometric modelling from single organisms to microbial communities.
Constraint-based stoichiometric modelling from single organisms to microbial communities.
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DOI：
10.1098/rsif.2016.0627
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发表时间：
2016-11
期刊：
影响因子：
--
通讯作者：
Teusink B
中科院分区：
文献类型：
--
作者：
Gottstein W;Olivier BG;Bruggeman FJ;Teusink B
微生物群落在自然界中无处不在，对环境、人类健康和生物技术有着直接的影响。微生物群落的种类组成和整体功能在很大程度上受资源竞争和交叉取食等代谢相互作用的影响。尽管在绘制和模拟物种水平代谢方面取得了相当大的科学进展，但阐明微生物之间的代谢交换并指导群落动态仍然是一个巨大的科学挑战。鉴于其复杂性，微生物群落的计算模型对于获得对生态系统功能的系统级理解至关重要。本文讨论了基于约束的化学计量建模工具的应用和局限性，特别是通量平衡分析（FBA）。我们从基本原理解释了这种方法，并确定了将其扩展到社区时面临的挑战，并根据这些挑战讨论了在该领域使用的方法。我们区分了扩展到社区的稳态和动态FBA方法。我们的结论是，已经取得了很大进展，但许多挑战仍然存在。
Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge. In view of the complexity, computational models of microbial communities are essential to obtain systems-level understanding of ecosystem functioning. This review discusses the applications and limitations of constraint-based stoichiometric modelling tools, and in particular flux balance analysis (FBA). We explain this approach from first principles and identify the challenges one faces when extending it to communities, and discuss the approaches used in the field in view of these challenges. We distinguish between steady-state and dynamic FBA approaches extended to communities. We conclude that much progress has been made, but many of the challenges are still open.
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