Highly multiplexed spatial transcriptomics in bacteria

作     者：Sarfatis, Ari Wang, Yuanyou Twumasi-Ankrah, Nana Moffitt, Jeffrey R. 

作者机构：Program in Cellular and Molecular Medicine Boston Children's Hospital Boston MA United States Department of Microbiology Harvard Medical School Boston MA United States Broad Institute of Harvard and MIT Cambridge MA United States 

出 版 物：《Science》 (Sci.)

年 卷 期：2025年第387卷第6732期

页      面：eadr0932页

学科分类：07[理学] 08[工学] 

基　　金：Harvard Cancer Center Pew Biomedical Scholars Program Dana-Farber Harvard Medical School, HMS Harvard Cancer Center in Boston Advanced Research Projects Agency for Health Massachusetts Host-Microbiome Center National Eye Institute, NEI, (EY012196) National Eye Institute, NEI National Cancer Institute, NCI, (P30CA06516) National Cancer Institute, NCI National Institutes of Health, USNIH, (R01GM143277, R21AI166230) National Institutes of Health, USNIH Harvard Digestive Diseases Center, Harvard University, HDDC, (P30DK034854) Harvard Digestive Diseases Center, Harvard University, HDDC 

摘      要：Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial messenger RNA. To overcome this challenge, we combined 1000-fold volumetric expansion with multiplexed error-robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH. This method enables high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissected the response of Escherichia coli to carbon starvation, systematically mapped subcellular RNA organization, and charted the adaptation of a gut commensal Bacteroides thetaiotaomicron to micrometer-scale niches in the mammalian colon. We envision that bacterial-MERFISH will be broadly applicable to the study of bacterial single-cell heterogeneity in diverse, spatially structured, and native environments. © 2025 American Association for the Advancement of Science. All rights reserved.