Peterson Joseph R, Cole John A, Luthey-Schulten Zaida
Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.
PLoS One. 2017 Aug 18;12(8):e0182570. doi: 10.1371/journal.pone.0182570. eCollection 2017.
Characterizing the complex spatial and temporal interactions among cells in a biological system (i.e. bacterial colony, microbiome, tissue, etc.) remains a challenge. Metabolic cooperativity in these systems can arise due to the subtle interplay between microenvironmental conditions and the cells' regulatory machinery, often involving cascades of intra- and extracellular signalling molecules. In the simplest of cases, as demonstrated in a recent study of the model organism Escherichia coli, metabolic cross-feeding can arise in monoclonal colonies of bacteria driven merely by spatial heterogeneity in the availability of growth substrates; namely, acetate, glucose and oxygen. Another recent study demonstrated that even closely related E. coli strains evolved different glucose utilization and acetate production capabilities, hinting at the possibility of subtle differences in metabolic cooperativity and the resulting growth behavior of these organisms. Taking a first step towards understanding the complex spatio-temporal interactions within microbial populations, we performed a parametric study of E. coli growth on an agar substrate and probed the dependence of colony behavior on: 1) strain-specific metabolic characteristics, and 2) the geometry of the underlying substrate. To do so, we employed a recently developed multiscale technique named 3D dynamic flux balance analysis which couples reaction-diffusion simulations with iterative steady-state metabolic modeling. Key measures examined include colony growth rate and shape (height vs. width), metabolite production/consumption and concentration profiles, and the emergence of metabolic cooperativity and the fractions of cell phenotypes. Five closely related strains of E. coli, which exhibit large variation in glucose consumption and organic acid production potential, were studied. The onset of metabolic cooperativity was found to vary substantially between these five strains by up to 10 hours and the relative fraction of acetate utilizing cells within the colonies varied by a factor of two. Additionally, growth with six different geometries designed to mimic those that might be found in a laboratory, a microfluidic device, and inside a living organism were considered. Geometries were found to have complex, often nonlinear effects on colony growth and cross-feeding with "hard" features resulting in larger effect than "soft" features. These results demonstrate that strain-specific features and spatial constraints imposed by the growth substrate can have significant effects even for microbial populations as simple as isogenic E. coli colonies.
描述生物系统（如细菌菌落、微生物群、组织等）中细胞间复杂的时空相互作用仍然是一项挑战。这些系统中的代谢协同作用可能源于微环境条件与细胞调节机制之间的微妙相互作用，通常涉及细胞内和细胞外信号分子的级联反应。在最简单的情况下，正如最近对模式生物大肠杆菌的研究所表明的，代谢交叉喂养可以在仅由生长底物（即乙酸盐、葡萄糖和氧气）可用性的空间异质性驱动的细菌单克隆菌落中出现。另一项最近的研究表明，即使是密切相关的大肠杆菌菌株也进化出了不同的葡萄糖利用和乙酸盐生产能力，这暗示了这些生物体在代谢协同作用以及由此产生的生长行为方面可能存在细微差异。为了初步了解微生物群体内复杂的时空相互作用，我们对大肠杆菌在琼脂底物上的生长进行了参数研究，并探究了菌落行为对以下因素的依赖性：1）菌株特异性代谢特征，以及2）底层底物的几何形状。为此，我们采用了一种最近开发的名为3D动态通量平衡分析的多尺度技术，该技术将反应扩散模拟与迭代稳态代谢建模相结合。所研究的关键指标包括菌落生长速率和形状（高度与宽度）、代谢物的产生/消耗和浓度分布，以及代谢协同作用的出现和细胞表型的比例。我们研究了五种密切相关的大肠杆菌菌株，它们在葡萄糖消耗和有机酸生产潜力方面表现出很大差异。发现这五种菌株之间代谢协同作用的开始时间相差多达10小时，并且菌落内利用乙酸盐的细胞的相对比例相差两倍。此外，还考虑了六种不同几何形状的生长情况，这些几何形状旨在模拟实验室、微流控设备和活生物体内可能出现的形状。发现几何形状对菌落生长和交叉喂养具有复杂的、通常是非线性的影响，“硬”特征比“软”特征产生的影响更大。这些结果表明，即使对于像同基因大肠杆菌菌落这样简单的微生物群体，菌株特异性特征和生长底物施加的空间限制也可能产生重大影响。
