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

在微米尺度上了解微生物群落的空间组织对于了解单个微生物的行为，它们的特性以及群落作为一个整体如何发挥作用至关重要。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。它的目标是开发鉴定存在的细菌的方法，使用与细菌核糖体的RNA结合的荧光探针，以保持细菌相对于彼此和相对于宿主生物体的微米级空间组织的方式。这些工具将帮助广大的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产生更广泛的影响，开发一套可交付成果，科学界可以采用并用于有利于畜牧业，水产养殖和健康的研究。其他更广泛的影响包括使微生物世界更容易为人们所理解，通过生成细菌建立在其宿主上的结构和群落的惊人图像;向初中和高中学生提供有关细菌群落的信息;帮助培养大学生，我们对微生物组的理解中的一个关键差距是普遍缺乏关于它们的微米尺度空间组织的信息，因为大多数工作都是在已经均质化的样品上进行的。一个微生物的邻居可以显着改变其生理，和微观尺度的空间组织提供线索的作用和相互作用的分类群，从而可以指导建模策略和更详细的研究生化相互作用。此外，空间结构可以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从中产生的高通量序列信息所掩盖。空间组织的成像可以穿透序列数据的巨大复杂性，并允许常见模式闪耀。这是一个开发适用于各种动物相关微生物的样品制备方案和荧光原位杂交探针的项目。其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.