Bacteriophages (phages) have been proposed as alternative therapeutics for the treatment of multidrug-resistant bacterial infections. However, there are major gaps in our understanding of the molecular events in bacterial cells that control how bacteria respond to phage predation. Using the model organism Enterococcus faecalis, we used two distinct genomic approaches, namely, transposon library screening and RNA sequencing, to investigate the interaction of E. faecalis with a virulent phage. We discovered that a transcription factor encoding a LytR family response regulator controls the expression of enterococcal polysaccharide antigen (epa) genes that are involved in phage infection and bacterial fitness. In addition, we discovered that DNA mismatch repair mutants rapidly evolve phage adsorption deficiencies, underpinning a molecular basis for epa mutation during phage infection. Transcriptomic profiling of phage-infected E. faecalis revealed broad transcriptional changes influencing viral replication and progeny burst size. We also demonstrate that phage infection alters the expression of bacterial genes associated with intra- and interbacterial interactions, including genes involved in quorum sensing and polymicrobial competition. Together, our results suggest that phage predation has the potential to influence complex microbial behavior and may dictate how bacteria respond to external environmental stimuli. These responses could have collateral effects (positive or negative) on microbial communities, such as the host microbiota, during phage therapy.IMPORTANCE We lack fundamental understanding of how phage infection influences bacterial gene expression and, consequently, how bacterial responses to phage infection affect the assembly of polymicrobial communities. Using parallel genomic approaches, we have discovered novel transcriptional regulators and metabolic genes that influence phage infection. The integration of whole-genome transcriptomic profiling during phage infection has revealed the differential regulation of genes important for group behaviors and polymicrobial interactions. Our work suggests that therapeutic phages could more broadly influence bacterial community composition outside their intended host targets.

中文翻译：

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平行基因组学揭示新型肠球菌噬菌体相互作用。

已经提出噬菌体（噬菌体）作为用于治疗多药耐药细菌感染的替代疗法。但是，在我们对细菌细胞中控制细菌如何对噬菌体捕食作出反应的分子事件的理解上，存在重大差距。使用模型生物粪肠球菌，我们使用了两种不同的基因组方法，即转座子文库筛选和RNA测序，来研究粪肠球菌与强毒噬菌体的相互作用。我们发现，编码LytR家族应答调节因子的转录因子控制参与噬菌体感染和细菌适应性的肠球菌多糖抗原（epa）基因的表达。此外，我们发现DNA错配修复突变体会迅速发展噬菌体的吸附缺陷，噬菌体感染过程中epa突变的分子基础。噬菌体感染的粪肠球菌的转录组分析显示，广泛的转录变化影响了病毒的复制和子代爆发大小。我们还证明噬菌体感染改变了与细菌内和细菌间相互作用相关的细菌基因的表达，包括参与群体感应和微生物竞争的基因。总之，我们的结果表明，噬菌体捕食有可能影响复杂的微生物行为，并可能决定细菌如何响应外部环境刺激。在噬菌体治疗期间，这些反应可能对微生物群落（例如宿主微生物群）产生附带影响（正面或负面）。重要性我们对噬菌体感染如何影响细菌基因表达以及因此细菌对噬菌体感染的反应如何影响多微生物群落的组装缺乏基本的了解。使用平行的基因组方法，我们发现了影响噬菌体感染的新型转录调节因子和代谢基因。噬菌体感染过程中全基因组转录组谱分析的整合揭示了对群体行为和微生物相互作用重要的基因的差异调节。我们的工作表明，治疗性噬菌体可以更广泛地影响其预期宿主目标以外的细菌群落组成。我们发现了影响噬菌体感染的新型转录调节因子和代谢基因。噬菌体感染过程中全基因组转录组谱分析的整合揭示了对群体行为和微生物相互作用重要的基因的差异调节。我们的工作表明，治疗性噬菌体可以更广泛地影响其预期宿主目标以外的细菌群落组成。我们发现了影响噬菌体感染的新型转录调节因子和代谢基因。噬菌体感染过程中全基因组转录组谱分析的整合揭示了对群体行为和微生物相互作用重要的基因的差异调节。我们的工作表明，治疗性噬菌体可以更广泛地影响其预期宿主目标以外的细菌群落组成。