EFRI-MIKS: Control of Signaling and Function by Design with Spatially Pre-Structured Microbial Communities

该项目旨在开发一个严格的工程框架，以加强对种间和界间信号的理解，以便能够构建“药丸中的微生物组”颗粒，精确设计，空间结构的微生物群落封装在生物相容性材料中，最终预防和治疗与生态失调（微生物失衡）相关的人类疾病。这个工程框架将通过解决四个挑战来预测和控制物种间的信号和体内和体外的相互作用：目标1 (MIKS1a)：使用计算方法来预测，对于给定的期望功能，需要哪些特定的微生物和实现该功能所需的空间结构。目标2 (MIKS1b和MIKS2)：发展体外微流体技术和相关设计原则，通过快速表征和测量空间结构对信号传导和宿主细胞基础的复杂分子相互作用的影响来理解信号传导？幻想的信号。目标3 (MIKS2和MIKS3)：开发和测试设计原则，用于扩大目标1和2中发现和表征的空间预结构微生物群落的规模，以实现体内测试所需的克量工程功能群落的生产。目标4(MIKS2和MIKS3)：通过使用目标3中产生的群落，并将其灌入无菌和非生物小鼠中，测量群落的体内功能和宿主的反应，并迭代目标1-3，制定一套设计规则，使空间预结构的“药丸微生物组”颗粒能够合理地在哺乳动物肠道中发挥可预测的作用。智力优势：多物种和跨界系统及其信号的重要性已得到广泛认可，但迫切需要控制此类系统的通用工程方法。该项目提出信号和相互作用可以通过对空间结构的仿生学方法控制来精确设计。这对于理解信号传导、代谢交换和群落功能如何受到控制是一个潜在的变革。哺乳动物微生物群是一个很好的测试系统，因为它包含了各种各样的物种，它们彼此之间以及宿主之间相互作用。这项工作将为“药丸中的微生物组”这一新的工程范式奠定基础，并为控制群落内部、群落与竞争对手之间以及群落与宿主之间的信号和代谢交换建立设计原则。具有空间结构的工程群落可以填补理解生态失调机制和控制受生态失调影响的群落的重要空白，最终导致更有效的预防和治疗人类疾病。组装的团队完全有资格开展拟议的工作：PI在微流体技术开发，以及生物背景下复杂网络的分析和建模方面具有专业知识。合著者迈耶和亨利是宏基因组数据集自动注释和使用这些注释来创建和分析基因组尺度代谢模型的专家。Chervonsky和Mazmanian是使用无菌和非生物动物模型来了解哺乳动物肠道微生物群对宿主免疫系统影响的专家。更广泛的影响：最终，在这项工作中设计的简单而精确的“药丸中的微生物组”社区可以通过调节影响数百万美国人的环境中的生态失调来显着提高生活质量并降低医疗成本：IBD，感染，糖尿病，自身免疫性疾病和肥胖。这种方法可能为转基因微生物不可接受或不可行的问题开辟新的解决方案。这里开发的构建功能性微生物群落的设计规则应该在人类健康之外产生广泛的影响，具有解决当今社会面临的许多问题的潜力，包括环境污染物、气候、食品和燃料生产，这些问题都受到微生物群落功能的强烈影响。该项目将为研究生、本科生和博士后学者提供教育、培训和指导，并加强PI在指导学生方面的优秀记录。该项目还将为研究人员提供许多工具来研究和利用微生物群落的特定功能。共同PI Meyer和Henry在传播计算方法和工具方面有着广泛的记录，PI在通过高影响力出版物和与行业合作伙伴关系传播知识方面有着出色的记录。该项目将通过REELScience支持公众宣传，通过加州理工学院课堂连接为K-12课程开发提供实践科学，并通过暑期研究连接为教师和高中生提供研究培训。

1137089IsmagilovThis project aims to develop a rigorous engineering framework to enhance understanding of interspeciesand interkingdom signaling in order to enable building of "microbiome in a pill" particles preciselyengineered, spatially structured microbial communities encapsulated in a biocompatible material toultimately prevent and treat human diseases associated with dysbiosis (microbial imbalance). Thisengineering framework will enable prediction and control of interspecies signaling and interactions both invitro and in vivo by solving four challenges: Goal 1 (MIKS1a): Use computational methods to predict, fora given desired function, which specific microbes are needed and which spatial structures are required toachieve that function. Goal 2 (MIKS1b and MIKS2): Develop in vitro microfluidic technologies andassociated design principles to understand signaling by rapidly characterizing and measuring the impactof spatial structure on the complex molecular interactions that underlie signaling, and host cells? responseto signaling. Goal 3 (MIKS2 and MIKS3): Develop and test design principles for the scale up of spatiallypre-structured microbial communities, discovered and characterized in Goals 1 and 2, to enableproduction of engineered functional communities in gram quantities needed for in vivo testing. Goal 4(MIKS2 and MIKS3): By using communities produced in Goal 3, and by gavaging them into germ-freeand gnotobiotic mice, measure in vivo the function of the community and the host's response, and iteratewith Goals 1-3 to develop a set of design rules that enable rational engineering of spatially pre-structured"microbiome in a pill" particles that predictably function in vivo in a mammalian gut.Intellectual Merit: The importance of multi-species and inter-kingdom systems and their signaling iswidely appreciated but general engineering approaches for control of such systems are urgently needed.This project proposes that signaling and interactions can be precisely engineered via a biomimeticapproach control of spatial structure. This is a potentially transformative shift in understanding howsignaling, metabolic exchange, and function of communities are controlled. The mammalian microbiomeis an excellent test system because it contains a diverse number of species interacting with one anotherand the host. This work will lay the foundation for a new engineering paradigm, a "microbiome in a pill",and establish design principles for controlling signaling and metabolic exchange within the community,between the community and competitors, and between the community and the host. Engineeringcommunities with spatial structure may close important gaps in understanding the mechanisms ofdysbiosis and manipulating communities affected by dysbiosis, ultimately leading to more effectiveprophylactics and treatments for human disease. The assembled team is well-qualified to carry out theproposed work: The PI has expertise in microfluidic technology development, and analysis and modelingof complex networks in biological contexts. Co-PIs Meyer and Henry are experts in automated annotationof metagenomic datasets and in using these annotations to create and analyze genome-scale metabolicmodels. Co-PIs Chervonsky and Mazmanian are experts in the use of germ-free and gnotobiotic animalmodels to understand the impact of microbiota in the mammalian gut on the host immune system.Broader Impact: Ultimately, the simple yet precisely engineered "microbiome in a pill" communitiesdesigned in this work could dramatically improve quality of life and reduce healthcare costs by modulatingdysbiosis in the context of conditions affecting millions of Americans: IBD, infections, diabetes,autoimmune conditions, and obesity. This approach may pioneer new solutions for problems wheregenetically modified microorganisms are not acceptable or feasible. The design rules for buildingfunctional microbial communities developed here should have broad impact outside of human health, withthe potential to address numerous issues facing society today, including environmental contaminants,climate, and food and fuel production, which are all strongly impacted by the function of microbialcommunities. The project will provide education, training, and mentoring for graduate and undergraduatestudents and postdoctoral scholars, enhanced by the PI's excellent track record in mentoring students.This project will also provide researchers with numerous tools to study and use microbial communities forspecific functions. Co-PIs Meyer and Henry have extensive track records in disseminating computationalmethods and tools, and the PI has an excellent track record of disseminating knowledge via high-impactpublications and partnerships with industry. This project will support public outreach through REELScience, hands-on science for K-12 curriculum development through CalTech Classroom Connection,and research training for teachers and high school students through the Summer Research Connection.