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Highly Multiplexed Spatial Mapping of Microbial Communities

View ORCID ProfileHao Shi, View ORCID ProfileWarren Zipfel, View ORCID ProfileIlana Brito, View ORCID ProfileIwijn De Vlaminck
doi: https://doi.org/10.1101/678672
Hao Shi
Department of Physics, Cornell University, Ithaca, NY, USANancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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  • For correspondence: hs673@cornell.edu vlaminck@cornell.edu
Warren Zipfel
Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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Ilana Brito
Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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Iwijn De Vlaminck
Department of Physics, Cornell University, Ithaca, NY, USANancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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  • For correspondence: hs673@cornell.edu vlaminck@cornell.edu
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ABSTRACT

Mapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density and rich diversity of species in environmental microbiomes and the limitations of optical imaging technology. Here, we introduce High Phylogenetic Resolution microbiome mapping by Fluorescence In-Situ Hybridization (HiPR-FISH), a versatile and cost-effective technology that uses binary encoding and spectral imaging and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrate the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli strains, each fluorescently labeled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and segmentation of single-cells in the native context of tissues, reveals the intricate spatial architectures formed by bacteria in the human oral plaque microbiome and disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment. HiPR-FISH provides a framework for analyzing the spatial organization of microbial communities in tissues and the environment at single cell resolution.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 21, 2019.
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Highly Multiplexed Spatial Mapping of Microbial Communities
Hao Shi, Warren Zipfel, Ilana Brito, Iwijn De Vlaminck
bioRxiv 678672; doi: https://doi.org/10.1101/678672
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Highly Multiplexed Spatial Mapping of Microbial Communities
Hao Shi, Warren Zipfel, Ilana Brito, Iwijn De Vlaminck
bioRxiv 678672; doi: https://doi.org/10.1101/678672

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