Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan.
Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan; Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10, Kita-ku, Sapporo Hokkaido 001-0020, Japan.
Genomics. 2021 May;113(3):1534-1542. doi: 10.1016/j.ygeno.2021.03.021. Epub 2021 Mar 24.
Enterococcus faecalis is a common human gut commensal bacterium. While some E. faecalis strains are probiotic, others are known to cause opportunistic infections, and clear distinction between these strains is difficult using traditional taxonomic approaches. In this study, we completed the genome sequencing of EF-2001, a probiotic strain, using our in-house hybrid assembly approach. Comparative analysis showed that EF-2001 was devoid of cytolysins, major factors associated with pathogenesis, and was phylogenetically distant from pathogenic E. faecalis V583. Genomic analysis of strains with a publicly available complete genome sequence predicted that drug-resistance genes- dfrE, efrA, efrB, emeA, and lsaA were present in all strains, and EF-2001 lacked additional drug-resistance genes. Core- and pan-genome analyses revealed a higher degree of genomic fluidity. We found 49 genes specific to EF-2001, further characterization of which may provide insights into its diverse biological activities. Our comparative genomic analysis approach could help predict the pathogenic or probiotic potential of E. faecalis leading to an early distinction based on genome sequences.
屎肠球菌是一种常见的人类肠道共生细菌。虽然有些屎肠球菌菌株是益生菌，但其他菌株已知会引起机会性感染，而使用传统的分类方法很难清楚地区分这些菌株。在这项研究中，我们使用内部混合组装方法完成了益生菌菌株 EF-2001 的基因组测序。比较分析表明，EF-2001 缺乏细胞溶解素，这是与发病机制相关的主要因素，并且与致病性屎肠球菌 V583 在系统发育上相距甚远。对具有公开可用完整基因组序列的菌株进行基因组分析预测，所有菌株都存在耐药基因 dfrE、efrA、efrB、emeA 和 lsaA，而 EF-2001 缺乏其他耐药基因。核心基因组和泛基因组分析显示出更高程度的基因组流动性。我们发现了 49 个特定于 EF-2001 的基因，对其进一步的表征可能有助于深入了解其多样化的生物学活性。我们的比较基因组分析方法可以帮助预测屎肠球菌的致病或益生菌潜力，从而可以根据基因组序列进行早期区分。
