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bioRxiv · 10.1101/2022.07.18.500470

Spatial host-microbiome sequencing

Lötstedt, B.·Strazar, M.·Xavier, R. J.·Regev, A.·Vickovic, S.
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Abstract

Mucosal and barrier tissues such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for our understanding of homeostasis and disease. Spatial transcriptomics has emerged as a key technology to positionally profile RNAs at high resolution in tissues. Here, we present spatial host-microbiome sequencing, an all-sequencing based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from tissues on spatially barcoded glass surfaces. We apply our approach to the mouse gut as a model system, use a novel deep learning approach for data mapping and detect spatial niches impacted by microbial biogeography. Spatial host-microbiome sequencing should enhance study of native host-microbe interactions in health and disease.

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Lötstedt, B., Strazar, M., Xavier, R. J., Regev, A., Vickovic, S.. 2022-07-19. Spatial host-microbiome sequencing. https://doi.org/10.1101/2022.07.18.500470

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