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

Marine Biological Laboratory, Woods Hole MA

Investigators

Abstract

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.