PAPM EAGER: Tools for Investigating Micron-Scale Spatial Organization of Microbial Communities

在微米尺度上理解微生物群落的空间组织对于理解单个微生物的行为、它们的特性以及整个群落的功能是至关重要的。该项目将开发用于调查一系列宿主相关微生物群落的空间组织的工具和协议。它的目标是开发识别细菌存在的方法，使用荧光探针结合细菌核糖体的RNA，以一种保持细菌相对于彼此和相对于宿主生物的微米尺度空间组织的方式。这些工具将帮助广大科学家更好地了解微生物群落是如何组织的，它们是如何工作的，以及它们如何影响宿主动物的生物学。该项目的主要目标是在开发一套可交付成果方面产生更广泛的影响，科学界可以采用这些成果并将其用于有利于动物农业、水产养殖和健康的研究。其他更广泛的影响包括，通过生成细菌赖以生存的结构和群落的惊人图像，使人们更容易理解微生物世界；向中学生和高中生提供有关细菌群落的信息；并帮助培训来自代表性不足群体的大学生学习微生物组科学。在我们对微生物组的理解中，一个关键的差距是普遍缺乏有关其微米尺度空间组织的信息，因为大多数工作都是在均质化的样品上完成的。微生物的邻居可以极大地改变其生理机能，微米尺度的空间组织为分类群的角色和相互作用提供了线索，从而可以指导建模策略和更详细的生化相互作用研究。此外，空间结构可能揭示不同微生物组之间的共性，这些共性目前被微生物组的复杂性和可变性以及由此产生的高通量序列信息所掩盖。空间组织的成像可以突破序列数据的压倒性复杂性，并允许共同的模式闪耀。这是一个开发样品制备方案和荧光原位杂交探针的项目，适用于各种各样的动物相关微生物组。目标是使更广泛的科学界能够利用荧光原位杂交和光谱成像方法来表征广泛的宿主相关微生物组中微生物群落的空间组织。

Understanding the spatial organization of microbial communities at micrometer scales is critical for understanding how individual microbes behave, what their properties are, and how the community as a whole functions. This project will develop tools and protocols for investigating the spatial organization of a range of host-associated microbial communities. Its goal is to develop methods for identifying the bacteria that are present, using fluorescent probes that bind to the RNA of the bacterial ribosome, in a way that preserves the micrometer-scale spatial organization of the bacteria relative to each other and relative to the host organism. These tools will help a broad community of scientists gain a better understanding of how microbial communities are organized and how they work, and how they affect the biology of the host animal. The major goal of this project is to have as a broader impact the development of a set of deliverables that the scientific community can adopt and use for research that will benefit animal agriculture, aquaculture, and health. Additional broader impacts include making the microbial world more understandable to people, by generating striking images of the structures and communities that bacteria build on and in their hosts; providing information about bacterial communities to middle- and high-school students; and helping to train college students from under-represented groups in microbiome science.A critical gap in our understanding of microbiomes is a widespread lack of information about their micron-scale spatial organization, as most work is done on samples that have been homogenized. A microbe's neighbors can dramatically alter its physiology, and micron-scale spatial organization provides clues to the roles and interactions of the taxa, and thus can guide modeling strategies and more detailed studies of biochemical interactions. In addition, spatial structure may reveal commonalities across disparate microbiomes, commonalities that are currently obscured by the complexity and variability of microbiomes and the high-throughput sequence information generated from them. Imaging of spatial organization can cut through the overwhelming complexity of sequence data, and allow common patterns to shine through. This is a project to develop sample preparation protocols and fluorescence in situ hybridization probes applicable to a wide variety of animal-associated microbiomes. The goal is to enable the wider scientific community to make use of fluorescence in situ hybridization and spectral imaging approaches to characterize spatial organization of the microbial community in a broad range of host-associated microbiomes.