Designing a Multifunctional Nanoculture System for High-throughput in situ Assessment of Microbial Communities

本研究旨在开发新的生物材料和工具来培养微生物，并在接近模拟微生物自然生长环境的条件下研究它们。目前的方法很少做到这一点，所以科学家们研究的是可以生长的微生物，而不是那些存在但不能在非自然条件下生长的微生物。因此，即使已知微生物存在，对大多数微生物的研究也很少。这阻碍了科学发现由微生物制成的新材料，这些材料在医疗保健、环境修复或工业用途中具有潜在的应用。在这项研究中，从各种天然来源分离的微生物将被封闭在比头发宽度还小的胶囊中。胶囊的组成将被设计成有利于封闭的微生物物种的生长和它们与外界环境的交流。这种新的“纳米培养系统”将用于研究封闭的微生物群落如何与自然环境中的“外部”微生物交流和相互作用，比如胃肠道中的微生物。这将通过将封装的微生物喂给没有肠道微生物的小鼠来测试，并确定纳米培养系统是否可以恢复胃肠道健康。这项研究的结果将产生新的能力来培养微生物，并从这些未被充分研究的微生物中开发出新的材料，这些材料有可能恢复肠道微生物群的平衡。该项目将使高中生接触到生物技术领域，发展他们的技术技能，并建立他们的专业网络，作为激励该领域未来职业发展的战略。本研究旨在利用微流体技术开发多功能纳米培养系统，作为微生物群落动态的高通量评估工具。纳米培养物是由聚（二甲基硅氧烷）膜制成的纳米升培养物，可以调节其渗透性。纳米培养物的机械、运输和磁性可以促进微生物群落在环境条件下的长期储存和孵化。因此，纳米培养是一种微型装置，能够消除与种间竞争相关的生长速度偏差，并保护微生物免受生物和化学伤害。软壳微胶囊可以容纳、培养和储存多种微生物，用于群落动态研究、挑战性物种的生长和为微生物组恢复提供特定群落。将建立一种技术来隔离和监测环境条件下合成或确定的微生物群落的动态。具体来说，将设计一个功能性住房，以表征合成群落的意外生态影响，并研究其控制递送在操纵各种微生物组方面的优势。功能性纳米培养在小鼠全身辐照模型中传递产生IL-2的益生菌的可行性将被确定。智力上的价值源于所提议的工作所寻求产生的知识体系。在完成拟议的研究后，我们期望通过提供一种替代策略来快速可靠地评估能够影响与人类健康相关的微生物组的合成群落的持久性、稳定性和安全交付，从而拥有垂直先进的基于微生物的技术。最后，拟议的项目是一个变革性的教育模式，将吸引来自代表性不足群体的学生和教师。它将促进活动，帮助学生发展新的技术技能，参加会议，制定他们的专业发展计划，并帮助9-12岁和本科生拥抱STEM职业。该奖项反映了美国国家科学基金会的法定使命，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。

PART 1: NON-TECHNICAL SUMMARYThis research aims to develop new biomaterials and tools to cultivate microorganisms and study them in conditions that closely mimic the environment in which they naturally grow. Current methods rarely do this, so scientists study microbes that can grow and not those present but unable to grow in nonnatural conditions. Therefore, most microorganisms are poorly studied, even if known to exist. This has impeded the scientific discovery of novel materials made by microorganisms that have potential applications in health care, environmental remediation, or industrial use. In this research, microbes isolated from various natural sources will be enclosed in capsules that are smaller than the width of a hair. The composition of capsule will be designed to facilitate the growth of the microbial species enclosed and their communication with the outside environment. This new ‘nanoculture system’ will be used to study how the enclosed microbial communities communicate and interact with ‘outside’ microorganisms a natural environment, like that in the gastrointestinal track. This will be tested by feeding the encapsulated microbes to mice without gut microbes and determining if the nanoculture system can restore gastrointestinal health. The results of this research will result in new capabilities to grow microorganisms and develop new materials from these understudied microbes with potential to restore balance to the gut’s microbiomes. The project will expose high school students to the field of biotechnology and develop their technical skills and seed their professional networks as strategies to inspire future careers in this area.PART 2: TECHNICAL SUMMARYThis research aims to harness a microfluidic-based technique to develop a multifunctional nanoculture system as a high-throughput assessment tool for microbial community dynamics. The nanocultures are nanoliter cultures made of poly(dimethylsiloxane) membranes, which can be manipulated for tunable permeability. The mechanical, transport, and magnetic properties of the nanocultures can facilitate the long-term storage and incubation of the microbial communities in environmental conditions. The nanocultures are thus microdevices capable of eliminating growth rate bias associated with interspecies competition and preserving microbes against biological and chemical insults. The soft-shelled microcapsules can harbor, culture, and store a multitude of microbes for purposes including community dynamics study, growth of challenging species, and the delivery of defined communities for microbiome restoration. A technology will be built to sequester and monitor the dynamics of synthetic or defined microbial consortia in environmental conditions. Specifically, a functional housing will be designed to characterize the unintended ecological impacts of the synthetic communities and to investigate the advantages of their controlled delivery in manipulating various microbiomes. The feasibility of the functional nanocultures for delivering a probiotic producing IL-2 in a mouse model of total body irradiation will be determined. The intellectual merit stems from the body of knowledge that the proposed work seeks to generate. Upon completion of the proposed research, we expect to have vertically advanced microbial-based technology by providing an alternative strategy to quickly and reliably assess the persistence, stability, and safe delivery of a synthetic community capable of impacting microbiomes relevant to human health. Finally, the proposed project is a transformative education model that will engage students and faculty from underrepresented groups. It will promote activities to help students develop new technical skills, participate in conferences, craft their professional development plan, and help 9-12 and undergraduate students embrace the STEM career.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.