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

PAPM EAGER：研究微生物群落微米级空间组织的工具

• 批准号: 1650141
• 负责人: Jessica Mark Welch
• 金额: $ 30万
• 依托单位: Marine Biological Laboratory
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-15 至 2019-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1650141&HistoricalAwards=false
• 关键词: PAPM; EAGER; Tools; Investigating; Micron

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.

了解以微米尺度的微生物群落的空间组织对于了解单个微生物的行为方式，其特性以及整个社区的整体功能至关重要。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。它的目标是使用与细菌核糖体的RNA结合的荧光探针开发用于鉴定存在的细菌的方法，以一种保留细菌相对于彼此和相对于宿主有机体的微米尺度空间组织的方式。这些工具将帮助广泛的科学家社区更好地了解微生物社区的组织方式，工作方式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更广泛地影响科学界可以采用和使用的一组可交付成果的发展，从而使动物农业，水产养殖和健康受益。更广泛的影响包括通过产生细菌在其宿主和宿主中建立的结构和社区的惊人图像来使人们更容易理解微生物世界；向中学和高中生提供有关细菌社区的信息；并帮助培训来自微生物科学中代表性不足的小组的大学生。我们对微生物组的理解的重要差距是广泛缺乏有关其微米级空间组织的信息，因为大多数工作都是对已被化为同质的样本进行的。微生物的邻居可以显着改变其生理，而微米级的空间组织为分类单元的角色和相互作用提供了线索，因此可以指导建模策略和对生化相互作用的更详细的研究。此外，空间结构可能揭示了不同微生物群体之间的共同点，这是由于微生物组的复杂性和可变性所掩盖的，以及从它们产生的高通量序列信息所掩盖的。空间组织的成像可以削减序列数据的绝大部分复杂性，并允许常见的模式发光。这是一个开发样品制备方案和荧光原位杂交探针的项目，适用于各种动物相关的微生物组。目的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，以在广泛的宿主相关微生物中表征微生物群落的空间组织。

项目成果

A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis

• DOI: 10.1128/msystems.00177-19
• 发表时间: 2019-05
• 期刊: mSystems
• 影响因子: 6.4
• 作者: H. Lutz;H. Lutz;S. T. Ramírez-Puebla;Lisa A Abbo;Amber Durand;Cathleen Schlundt;N. Gottel;Alexandra K. Sjaarda;R. Hanlon;J. Gilbert;J. Gilbert;J. M. Welch