研究人员表示，复杂环境中的单细胞决策是许多细菌现象的基础。基于图像的转录组学方法为研究这些行为提供了途径，但这些方法受到细菌信使RNA密度过高的限制。为了克服这一挑战，研究人员将1000倍体积扩展，与多重错误鲁棒的荧光原位杂交（MERFISH）相结合，创造了细菌-MERFISH方法。
该方法能够在单个细菌中进行高通量、空间分辨的操作子剖面分析。使用细菌-MERFISH，研究人员解析了大肠杆菌对碳饥饿的反应，系统地绘制了亚细胞RNA的组织，并描绘了肠道共生菌Bacteroides thetaiotaomicron在哺乳动物结肠微米级生态位中的适应过程。
研究人员预计，细菌-MERFISH将广泛应用于研究细菌单细胞异质性，特别是在多样化、空间结构化和天然环境中的研究。
附：英文原文
Title: Highly multiplexed spatial transcriptomics in bacteria
Author: Ari Sarfatis, Yuanyou Wang, Nana Twumasi-Ankrah, Jeffrey R. Moffitt
Issue&Volume: 2025-01-24
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 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.
DOI: adr0932
Source: https://www.science.org/doi/10.1126/science.adr0932