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

生物技术对国家对科学进步的兴趣以及在生物制造、生物医学研究、可再生能源、可持续发展和食品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以单一培养为主，但利用合成微生物群落在生物技术中的许多应用具有巨大的潜力，包括生产高价值化学品。然而，缺乏对这些社区关键属性的有效控制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，并制定改进重要化学品生产的战略。此外，该项目将提供让高中生、本科生和研究生参与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的自动化动态调节。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和可逆地添加或移除光。在这个项目中，光遗传学将被用来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微生物群落代谢状态的即时反馈，以告知光遗传执行器，建立闭环反馈控制。这一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作生物合成途径的贡献。它还将有助于确定在整个共培养过程中的最佳群落组成，尽管有超级最佳的接种量或系统扰动。此外，该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，并能够感知生物合成途径中间体或最终产品的群落。该项目将为从根本上了解合成微生物群落的复杂行为提供新的机会。该项目由ENG/CBET中的细胞和生化工程、生物传感和生物光子学计划以及BIO/MCB中的系统和合成生物学计划共同支持。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.