PCR primers used to identify induced prophages.

Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome.由于大肠杆菌（Escherichia coli）常与尿路感染（urinary tract infections, UTIs）相关联，它是泌尿微生物组（urobiome）中特征最为明确的组成成分。然而，尿路致病性大肠杆菌仅是泌尿微生物组的一员。除细菌组分外，健康个体与有症状个体的泌尿微生物组中均存在多样化的细菌病毒群体——噬菌体（bacteriophages）。此前一项研究发现，泌尿微生物组中的多数细菌均为溶原菌（lysogens），其基因组中整合有一个或多个噬菌体，即前噬菌体（prophages）。其中多数前噬菌体为温和噬菌体（temperate phages），可进入裂解周期（lytic cycle）并裂解其细菌宿主。从溶原周期向裂解周期的转变，会对泌尿微生物组的细菌多样性产生影响。尽管诸多感染大肠杆菌的噬菌体，即大肠杆菌噬菌体（coliphages），已在实验室环境中被研究数十年，但泌尿微生物组内的大肠杆菌噬菌体尚未被编目。本研究首先对所有公开可用的泌尿大肠杆菌基因组中的前噬菌体进行鉴定，以此探究泌尿大肠杆菌噬菌体的多样性。我们共检测到3038条完整的前噬菌体序列，对应1542种独特的噬菌体。这些噬菌体既包含新发现的物种，也包括可在肠道微生物组中找到的物种。我们从本次分析包含的泌尿大肠杆菌菌株中分离得到10种温和噬菌体，并评估了它们感染并裂解泌尿大肠杆菌菌株的能力。此外，我们还在宿主范围测定（host range assays）中纳入了其他泌尿大肠杆菌噬菌体以及实验室常用的大肠杆菌噬菌体。结果显示，本次研究的温和噬菌体与其他泌尿大肠杆菌噬菌体均可有效裂解泌尿大肠杆菌菌株。我们还观察到，非泌尿来源的大肠杆菌噬菌体在裂解泌尿大肠杆菌菌株时效率最高。其中T2与N4这两种噬菌体可裂解83.5%（n = 86）的从出现尿路感染症状的女性体内分离得到的菌株。综上，本研究发现泌尿微生物组中存在多样化的大肠杆菌噬菌体群落，其中多数被预测为温和噬菌体，本研究已证实其中10种。它们感染并裂解泌尿大肠杆菌菌株的能力表明，泌尿大肠杆菌噬菌体可能在调节泌尿微生物组的大肠杆菌菌株多样性中发挥作用。