CAREER: Uncovering new rules of multicellular life using synthetic microbial communities

细胞是生命的基本组成部分。然而，自然界中的细胞很少单独生活，而是居住在被称为生物膜的组织或微生物群落中。一个引人注目的生物学问题是确定什么样的生命规则支配着从单个细胞的集合到多细胞群落的转变。生物膜被用作解决这个问题的模型，因为它们是由数百万个单细胞细菌组成的结构化群落，这些细菌表现出紧急协调和动态细胞间信号传导，让人想起多细胞生物。总体目标是了解细菌生物膜社区中由细胞间信号传导机制引起的紧急协调群体行为，以及这些紧急行为如何赋予功能性社区水平的益处。该项目使用合成微生物群落系统地构建混合生物膜，可以使用微流体技术以单细胞分辨率进行量化。借助于数学模型，乙酰胆碱信号动力学映射到一组混合生物膜种群的膜电压变化。了解细菌群落如何协调以应对其环境，可以提供一个尚未开发的新生物学来源，可以用于基础科学和生物医学应用。这种新的理解可以应用于一系列情况，从克服生物膜抗生素耐药性到使用合成生物学开发体内微生物诊断。这个多学科研究项目还为系统和合成生物学的学生提供了定量培训机会的肥沃土壤，并吸引学生利用微生物群落的最新研究来追求新的科学探究领域。虽然微生物学家长期以来一直在研究单独细菌培养物中的基因调控和代谢，并已开始描述生物膜水平的形态和模式形成，将这两个尺度结合起来是一个挑战。在这里，使用最近开发的荧光蛋白生物传感器，PI已经发现了协调的时空振荡的新代谢产物，自发出现在生物膜的发展。由于这些代谢物中的许多在细菌中缺乏已知的功能作用，这一发现提供了一个模型现象，以询问以前未探索的细胞间信号传导机制如何引起生物膜中的协调群体行为。具体而言，PI正在使用合成微生物群落系统地构建混合生物膜，并使用微流体技术以单细胞分辨率进行定量。借助于数学模型，时空代谢动力学映射到每个混合生物膜群体的膜电压变化。这些测量用于破译这些代谢物如何与电化学信号相互作用以增加生物膜适应性的机制基础。通过结合定量测量技术和易于处理的多细胞动力学模型系统，这项研究有望揭示多细胞生命的新规则。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The cell is the basic building block of life. However, cells in nature rarely live alone, but instead reside in communities such as tissues or microbial communities known as biofilms. A compelling biological problem is the determination of what rules of life govern the transition from a collection of individual cells to a multicellular community. Biofilms are used as a model to address this problem since they are structured communities composed of millions of single-celled bacteria that exhibit emergent coordination and dynamic cell-to-cell signaling reminiscent of multicellular organisms. The overarching goal is to understand the emergent coordinated group behaviors in bacterial biofilm communities that arise from cell-to-cell signaling mechanisms, and how these emergent behaviors impart functional community-level benefits. The project uses synthetic microbial communities to systematically construct mixed biofilms that can be quantified with single-cell resolution using microfluidics. Aided by a mathematical model, acetylcholine signaling dynamics is mapped to changes in membrane voltage for a set of mixed biofilm populations. Understanding how bacterial communities are coordinated to respond to their environments could provide an untapped source of new biology that could be harnessed for both basic science and biomedical applications. This new understanding could be applied to a range of circumstances from overcoming biofilm antibiotic resistance to developing in vivo microbial diagnostics using synthetic biology. This multidisciplinary research project also provides fertile ground for quantitative training opportunities for students in systems and synthetic biology and attracts students into pursuing new areas of scientific inquiry using the latest research on microbial communities.While microbiologists have long studied gene regulation and metabolism in solitary bacterial cultures and have begun to describe biofilm-level morphology and pattern formation, integrating these two scales has been challenging. Here, using recently developed fluorescent protein biosensors, the PI has uncovered coordinated spatiotemporal oscillations in novel metabolites that spontaneously emerge during biofilm development. Since many of these metabolites lack known functional roles in bacteria, this discovery provides a model phenomenon to interrogate how previously unexplored cell-to-cell signaling mechanisms give rise to coordinated group behavior in biofilms. Specifically, the PI is using synthetic microbial communities to systematically construct mixed biofilms that are quantified with single-cell resolution using microfluidics. Aided by a mathematical model, spatiotemporal metabolic dynamics are mapped to changes in membrane voltage for each mixed biofilm population. These measurements are used to decipher the mechanistic basis for how these metabolites interface with electrochemical signaling to increase biofilm fitness. By combining quantitative measurement techniques and a tractable model system for multicellular dynamics, this research is poised to uncover new rules of multicellular life.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.