Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.
Inria Saclay, Ile-de-France, Palaiseau, 91120, France.
Nat Commun. 2017 Nov 16;8(1):1535. doi: 10.1038/s41467-017-01683-1.
Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.
群体中的细菌在个体上存在差异，并与其他细菌和环境相互作用，从而产生群体水平的基因表达模式。详细研究这种行为需要在单细胞水平上测量和控制种群，同时精确指定相互作用和环境特征。在这里，我们提出了一个自动化、可编程的平台，该平台将基于图像的基因表达和生长测量与在线光遗传学表达控制相结合，可在动态可调环境中对数百个单个大肠杆菌细胞进行长达数天的实验。这个集成平台广泛地实现了将个体和群体行为联系起来的实验。我们证明了：（i）通过对许多单个细胞中的基因表达进行独立的闭环控制来实现群体结构；（ii）在抗生素扰动过程中对细胞间的变异性进行控制；（iii）在单个细胞中实现混合生物数字电路，以及在个体细菌之间进行自由指定的数字通信。这些例子展示了将理论模型与对许多单个细胞的测量和控制实时整合起来，以研究和设计微生物群体行为的潜力。
