Bacteria respond to changes in their environment with specific transcriptional programmes, but even within genetically identical populations these programmes are not homogenously expressed¹. Such transcriptional heterogeneity between individual bacteria allows genetically clonal communities to develop a complex array of phenotypes¹, examples of which include persisters that resist antibiotic treatment and metabolically specialized cells that emerge under nutrient-limiting conditions². Fluorescent reporter constructs have played a pivotal role in deciphering heterogeneous gene expression within bacterial populations³ but have been limited to recording the activity of single genes in a few genetically tractable model species, whereas the vast majority of bacteria remain difficult to engineer and/or even to cultivate. Single-cell transcriptomics is revolutionizing the analysis of phenotypic cell-to-cell variation in eukaryotes, but technical hurdles have prevented its robust application to prokaryotes. Here, using an improved poly(A)-independent single-cell RNA-sequencing protocol, we report the faithful capture of growth-dependent gene expression patterns in individual Salmonella and Pseudomonas bacteria across all RNA classes and genomic regions. These transcriptomes provide important reference points for single-cell RNA-sequencing of other bacterial species, mixed microbial communities and host–pathogen interactions.

细菌通过特定的转录程序来响应其环境的变化，但是即使在遗传上相同的种群中，这些程序也不是同质表达的¹。单个细菌之间的这种转录异质性使基因克隆群落能够发展出一系列复杂的表型¹，其实例包括抵抗抗生素治疗的持久性和在营养限制条件下出现的代谢专用细胞²。荧光报告基因构建体在破译细菌种群中的异源基因表达中发挥了关键作用³但仅限于记录一些在遗传上可控制的模型物种中单个基因的活性，而绝大多数细菌仍然难以工程改造和/或什至难以培养。单细胞转录组学正在彻底改变真核生物表型细胞间变异的分析方法，但是技术上的障碍阻止了其在原核生物中的稳健应用。在这里，使用改进的独立于poly（A）的单细胞RNA测序协议，我们报告了在沙门氏菌和假单胞菌中忠实捕获依赖于生长的基因表达模式所有RNA类和基因组区域的细菌。这些转录组为其他细菌种类，混合微生物群落和宿主-病原体相互作用的单细胞RNA测序提供了重要的参考点。