Johnson Genevieve, Wolfe Alan J, Putonti Catherine
Bioinformatics Program, Loyola University Chicago, Chicago, IL USA.
Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL USA.
Access Microbiol. 2019;1(1). doi: 10.1099/acmi.0.000002. Epub 2019 Mar 20.
Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of cultured from a kidney stone. Dobby is capable of lysing clinical strains within our collection from the urinary tract. Sequencing was performed producing a 37,152 bp genome that closely resembles the temperate phage ϕCTX, a member of the P2 phage group. Dobby does not, however, encode for the cytotoxin CTX. Dobby's genome was queried against publicly available bacterial sequences identifying 44 other ϕCTX-like prophages. These prophages are integrated within the genomes of strains from a variety of environments, including strains isolated from urine samples and other niches of the human body. Phylogenetic analysis suggests that the temperate ϕCTX phage species is widespread. With the isolation of Dobby, we now have evidence that phages are members of the kidney stone microbiota. Further investigation, however, is needed to determine their abundance and diversity within these communities.
噬菌体是人类微生物群的重要成员。即使在人体低生物量生态位中，包括下尿路，它们也很丰富。虽然之前有几项研究从肾结石中培养出了细菌，但这是第一项探索肾结石微生物群中噬菌体的研究。在此，我们报告了多比，一种从一株从肾结石中培养出的菌株分离出的温和噬菌体。多比能够裂解我们从尿路收集的临床菌株。进行了测序，产生了一个37152碱基对的基因组，该基因组与温和噬菌体ϕCTX非常相似，ϕCTX是P2噬菌体组的成员。然而，多比并不编码细胞毒素CTX。将多比的基因组与公开可用的细菌序列进行比对，鉴定出另外44个类似ϕCTX的原噬菌体。这些原噬菌体整合在来自各种环境的菌株基因组中，包括从尿液样本和人体其他生态位分离出的菌株。系统发育分析表明，温和的ϕCTX噬菌体种类广泛。随着多比的分离，我们现在有证据表明噬菌体是肾结石微生物群的成员。然而，需要进一步研究以确定它们在这些群落中的丰度和多样性。
