Spatial host-microbiome sequencing
Spatial host-microbiome sequencing
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.
L?tstedt Britta、Vickovic Sanja、Xavier Ramnik、Regev Aviv、Stra?ar Martin
Klarman Cell Observatory, Broad Institute of MIT and Harvard||Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of TechnologyKlarman Cell Observatory, Broad Institute of MIT and Harvard||New York Genome Center||Department of Biomedical Engineering and Herbert Irving Institute for Cancer Dynamics, Columbia University||Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala UniversityBroad Institute of MIT and Harvard||Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology||Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical SchoolKlarman Cell Observatory, Broad Institute of MIT and Harvard||Department of Biology, Massachusetts Institute of Technology||Genentech, 1 DNA WayBroad Institute of MIT and Harvard
微生物学生物科学研究方法、生物科学研究技术基础医学
L?tstedt Britta,Vickovic Sanja,Xavier Ramnik,Regev Aviv,Stra?ar Martin.Spatial host-microbiome sequencing[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/2022.07.18.500470.点此复制
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