Department of Biomedical Engineering, Columbia University, New York City, NY, USA.
Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.
Nat Chem Biol. 2023 Jul;19(7):878-886. doi: 10.1038/s41589-023-01325-2. Epub 2023 May 4.
A diverse array of bacteria species naturally self-organize into durable macroscale patterns on solid surfaces via swarming motility-a highly coordinated and rapid movement of bacteria powered by flagella. Engineering swarming is an untapped opportunity to increase the scale and robustness of coordinated synthetic microbial systems. Here we engineer Proteus mirabilis, which natively forms centimeter-scale bullseye swarm patterns, to 'write' external inputs into visible spatial records. Specifically, we engineer tunable expression of swarming-related genes that modify pattern features, and we develop quantitative approaches to decoding. Next, we develop a dual-input system that modulates two swarming-related genes simultaneously, and we separately show that growing colonies can record dynamic environmental changes. We decode the resulting multicondition patterns with deep classification and segmentation models. Finally, we engineer a strain that records the presence of aqueous copper. This work creates an approach for building macroscale bacterial recorders, expanding the framework for engineering emergent microbial behaviors.
多种多样的细菌物种通过群体运动自然地在固体表面上自我组织成持久的宏观模式-一种由鞭毛驱动的高度协调和快速的细菌运动。工程化群体运动是增加协调合成微生物系统规模和鲁棒性的未开发机会。在这里，我们对天然形成厘米级靶心群体模式的奇异变形杆菌进行工程改造，将外部输入“写入”可见的空间记录中。具体来说，我们对与群体运动相关的基因进行了可调节的表达，这些基因可以修饰模式特征，并且我们开发了定量方法来进行解码。接下来，我们开发了一种双输入系统，可以同时调节两个与群体运动相关的基因，并且我们分别表明，生长的菌落可以记录动态环境变化。我们使用深度学习分类和分割模型对生成的多条件模式进行解码。最后，我们设计了一种可以记录水合铜存在的菌株。这项工作创建了一种构建宏观细菌记录器的方法，扩展了用于工程突发微生物行为的框架。
