Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium
Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium
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DOI：
10.1016/j.ygeno.2021.03.021
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发表时间：
2021-03-31
期刊：
影响因子：
4.4
通讯作者：
Sekimizu, Kazuhisa
中科院分区：
文献类型：
--
作者：
Panthee, Suresh;Paudel, Atmika;Sekimizu, Kazuhisa
粪肠球菌是一种常见的人类肠道寄生菌。而一些E.粪肠球菌菌株是益生菌，已知其它菌株引起机会性感染，并且使用传统的分类学方法很难在这些菌株之间进行明确区分。在这项研究中，我们完成了EF-2001，益生菌菌株的基因组测序，使用我们的内部杂交组装方法。比较分析表明，EF-2001不含与致病相关的主要因子溶细胞素，与致病性大肠杆菌在遗传学上距离较远。faecalis V583.对具有公开可用的完整基因组序列的菌株的基因组分析预测，所有菌株中都存在耐药基因- dfrE、efrA、efrB、emeA和lsaA，EF-2001缺乏额外的耐药基因。核心基因组和泛基因组分析揭示了更高程度的基因组流动性。我们发现了49个EF-2001的特异性基因，进一步表征这些基因可能有助于了解EF-2001的多种生物活性。我们的比较基因组分析方法可以帮助预测致病性或益生潜力的E。faecalis导致基于基因组序列的早期区分。
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.