Collaborative Research: Closed-loop control of microbial communities by integrating optogenetics and metabolite biosensing

生物技术对于国家在科学进步方面的利益以及在生物制造、生物医学研究、可再生能源、可持续性和粮食生产等关键战略领域保持世界领先地位至关重要。虽然微生物生物过程主要由单一培养物控制，但合成微生物群落的利用在生物技术的许多应用中具有巨大的潜力，包括高价值化学品的生产。然而，缺乏有效的控制这些社区的关键属性阻碍了这一研究领域的发展。该项目将使用代谢物生物传感器和新型光遗传生长控制系统来调节微生物群落组成，并增加所需化学产品的产量。该项目将产生新的知识和方法，以推进合成微生物群落的基础研究，并制定改善重要化学品生产的战略。此外，该项目将为高中生、本科生和研究生提供参与STEM教育的绝佳机会。该项目的总体目标是整合光遗传控制和代谢物生物传感，以实现前所未有的微生物群落自动动态调节。光遗传学提供了用光控制生物功能的独特能力，可以按照任何规定的时间表立即可逆地添加或移除。在这个项目中，光遗传学将用于调节目标微生物的生长，并最终调整对生物生产的贡献。代谢物生物传感将提供关于微生物群落代谢状态的即时反馈，以通知光遗传学执行器，建立闭环反馈控制。这种首创的控制系统将用于设计微生物群落成员之间的相互作用及其对协同生物合成途径的贡献。它也将有助于确定最佳的社区组成，尽管超最佳接种或系统扰动整个共培养培养。此外，本项目将探索闭环控制在具有不同特征的群落中的应用，例如由相同或不同物种的成员组成的群落，包含线性或非线性生物合成途径，以及能够感知生物合成途径中间体或最终产物。该项目将为获得对合成微生物群落复杂行为的基本了解提供新的机会。 该项目由ENG/CBET的细胞和生物化学工程、生物传感和生物光子学项目以及BIO/MCB的系统和合成生物学项目共同支持。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。

Biotechnology is essential to the nation’s interest in scientific progress and maintaining world leadership in key strategic areas such as biomanufacturing, biomedical research, renewable energy, sustainability, and food production. While microbial bioprocesses are dominated by monocultures, utilization of synthetic microbial communities holds enormous potential for many applications in biotechnology, including production of high value chemicals. However, the lack of effective controls over key attributes of these communities impedes the development of this research field. This project will use metabolite biosensors and novel optogenetic growth control systems to modulate microbial community composition and to increase production of the desired chemical products. This project will generate new knowledge and methods to advance basic research in synthetic microbial communities and generate strategies for improved production of important chemicals. Moreover, this project will offer outstanding opportunities to engage high school, undergraduate, and graduate students in STEM education.The overall goal of this project is to integrate optogenetic controls and metabolite biosensing to achieve unprecedented automated dynamic regulation of microbial communities. Optogenetics offers the unique ability to control biological functions with light, which can be added or removed instantly and reversibly following any prescribed schedule. For this project, optogenetics will be used to modulate the growth of targeted microbes and ultimately to adjust contributions to bioproduction. Metabolite biosensing will provide instant feedback on the metabolic state of microbial communities to inform optogenetic actuators, establishing closed-loop feedback controls. This first-of-its-kind control system will be used to engineer interactions between members of microbial communities and their contributions towards collaborative biosynthetic pathways. It will also help identify the optimal community compositions throughout co-culture cultivation despite sup-optimal inoculums or system perturbations. Moreover, this project will explore the application of closed-loop controls in communities with different features, such as communities comprising members of the same or different species, containing linear or non-linear biosynthesis pathways, and capable of sensing biosynthetic pathway intermediates or final products. This project will open new opportunities to gain fundamental understanding of complex behaviors of synthetic microbial communities. This project is jointly supported by the Cellular and Biochemical Engineering, Biosensing and Biophotonics Programs in ENG/CBET, and the Systems and Synthetic Biology Program in BIO/MCB.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.