Year: 2025
Type: article
Abstract: 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 mRNA. To overcome this challenge, we combine 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 dissect the response of E. coli to carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of a gut commensal B. thetaiotaomicron to micron-scale niches in the mammalian colon. We envision bacterial-MERFISH will be broadly applicable to the study of bacterial single-cell heterogeneity in diverse, spatially structured, and native environments.
Source: Science
Institutions: Boston Children's Hospital, Harvard University, Broad Institute
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: Dana-Farber/Harvard Cancer Center, National Institutes of Health, Advanced Research Projects Agency, Harvard Digestive Diseases Center, Harvard University, National Human Genome Research Institute, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases
Awards: Rapid, Robust, and Routine: Multiplexed Microscopy for Spatially Resolved Whole-Transcriptomic Single-Cell Profiling and the Construction of Cell Atlases of all Tissues and in all Organisms, G5857948765, A spatially resolved single-cell transcriptomic technique for microbial pathogenesis, Integrated Epithelial and Muscosal Biology, Training in Bioinformatics and Integrative Genomics, Dana-Farber/Harvard Cancer Center
OpenAlex ID: W4406753301