In the last decade, powerful high-throughput sequencing approaches have emerged to analyse microbial transcriptomes at a global scale. However, to date, applications of these approaches to microbial viruses such as phages remain scarce. Tailoring these techniques to virus-infected bacteria promises to obtain a detailed picture of the underexplored RNA biology and molecular processes during infection. In addition, transcriptome study of stress and perturbations induced by phages in their infected bacterial hosts is likely to reveal new fundamental mechanisms of bacterial metabolism and gene regulation. Here, we provide references and blueprints to implement emerging transcriptomic approaches towards addressing transcriptome architecture, RNA–RNA and RNA–protein interactions, RNA modifications, structures and heterogeneity of transcription profiles in infected cells that will provide guides for future directions in phage-centric therapeutic applications and microbial synthetic biology.

在过去的十年中，出现了强大的高通量测序方法来在全球范围内分析微生物转录组。然而，迄今为止，这些方法在噬菌体等微生物病毒上的应用仍然很少。针对病毒感染的细菌定制这些技术有望获得感染过程中尚未充分探索的 RNA 生物学和分子过程的详细图片。此外，对噬菌体在受感染的细菌宿主中引起的应激和扰动进行转录组研究可能会揭示细菌代谢和基因调控的新基本机制。在这里，我们提供参考和蓝图来实施新兴的转录组学方法，以解决受感染细胞中转录组结构、RNA-RNA 和 RNA-蛋白质相互作用、RNA 修饰、转录谱的结构和异质性，这将为以噬菌体为中心的治疗的未来方向提供指导应用和微生物合成生物学。