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Microbial single-cell RNA sequencing by split-pool barcoding
Science ( IF 56.9 ) Pub Date : 2021-02-19 , DOI: 10.1126/science.aba5257
Anna Kuchina 1 , Leandra M Brettner 2, 3 , Luana Paleologu 4, 5 , Charles M Roco 2 , Alexander B Rosenberg 1 , Alberto Carignano 1 , Ryan Kibler 6 , Matthew Hirano 1 , R William DePaolo 3, 7 , Georg Seelig 1, 8, 9
Affiliation  

Single-cell RNA sequencing (scRNA-seq) has become an essential tool for characterizing gene expression in eukaryotes, but current methods are incompatible with bacteria. Here, we introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for Gram-negative and Gram-positive bacteria that can resolve heterogeneous transcriptional states. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating an atlas of changes in metabolism and lifestyle. We retrieved detailed gene expression profiles associated with known, but rare, states such as competence and prophage induction and also identified unexpected gene expression states, including the heterogeneous activation of a niche metabolic pathway in a subpopulation of cells. MicroSPLiT paves the way to high-throughput analysis of gene expression in bacterial communities that are otherwise not amenable to single-cell analysis, such as natural microbiota.



中文翻译:

通过拆分池条形码进行微生物单细胞 RNA 测序

单细胞 RNA 测序 (scRNA-seq) 已成为表征真核生物基因表达的重要工具,但目前的方法与细菌不相容。在这里,我们介绍了 microSPLiT(微生物分裂池连接转录组学),这是一种用于革兰氏阴性和革兰氏阳性细菌的高通量 scRNA-seq 方法,可以解决异质转录状态。我们将 microSPLiT 应用于 >25,000枯草芽孢杆菌在不同生长阶段对细胞进行采样,创建新陈代谢和生活方式变化的图谱。我们检索了与已知但罕见的状态(如能力和原噬菌体诱导)相关的详细基因表达谱,还确定了意外的基因表达状态,包括细胞亚群中生态位代谢途径的异质激活。MicroSPLiT 为细菌群落中基因表达的高通量分析铺平了道路,否则这些群落不适合单细胞分析,例如天然微生物群。

更新日期:2021-02-19
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