Harcombe William R, Riehl William J, Dukovski Ilija, Granger Brian R, Betts Alex, Lang Alex H, Bonilla Gracia, Kar Amrita, Leiby Nicholas, Mehta Pankaj, Marx Christopher J, Segrè Daniel
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA.
Cell Rep. 2014 May 22;7(4):1104-15. doi: 10.1016/j.celrep.2014.03.070. Epub 2014 May 1.
The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of microbial communities. This raises the question of whether ecosystem-level behavior of structured communities can be predicted using genome-scale metabolic models for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice and applied it to engineered communities. First, we predicted and experimentally confirmed the species ratio to which a two-species mutualistic consortium converges and the equilibrium composition of a newly engineered three-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the "eclipse dilemma": does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding that the net outcome is beneficial highlights the complex nature of metabolic interactions in microbial communities while at the same time demonstrating their predictability.
代谢物的种间交换在微生物群落的时空动态中起着关键作用。这就提出了一个问题，即是否可以使用多种生物体的基因组规模代谢模型来预测结构化群落的生态系统水平行为。我们开发了一个建模框架，该框架将动态通量平衡分析与晶格上的扩散相结合，并将其应用于工程群落。首先，我们预测并通过实验证实了两物种互利共生聚集体收敛到的物种比例以及新工程化的三成员群落的平衡组成。接下来，我们确定了菌落的一种特定空间排列，这导致了我们所说的“日食困境”：置于一个菌落与其交叉喂养伙伴之间的竞争者对原始菌落的生长是有益还是有害？我们通过实验验证的结果表明净结果是有益的，这突出了微生物群落中代谢相互作用的复杂性，同时也证明了它们的可预测性。
