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

了解微生物群落在微米尺度上的空间组织对于了解单个微生物的行为、它们的性质以及群落作为一个整体是如何运作的至关重要。该项目将开发工具和协议，以调查一系列与宿主相关的微生物群落的空间组织。它的目标是开发识别存在的细菌的方法，使用与细菌核糖体RNA结合的荧光探针，以保存细菌相对于彼此和相对于宿主有机体的微米尺度的空间组织。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，以及它们是如何影响宿主动物的生物学的。该项目的主要目标是对一系列成果的开发产生更广泛的影响，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醒目图像，使人们更容易理解微生物世界；向初中生和高中生提供关于细菌群落的信息；帮助培训来自未被充分代表的群体的大学生微生物群科学。我们对微生物群理解的一个关键差距是普遍缺乏关于其微米尺度空间组织的信息，因为大多数工作都是在已均质的样本上完成的。微生物的邻居可以极大地改变其生理，而微米级的空间组织提供了分类群的作用和相互作用的线索，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群之间的共性，目前被微生物群及其产生的高通量序列信息的复杂性和变异性所掩盖的共性。空间组织的成像可以穿透序列数据的压倒性复杂性，并允许常见的模式显现出来。这是一个项目，旨在开发适用于多种动物相关微生物群的样品制备方案和荧光原位杂交探针。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与宿主相关的广泛微生物群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.