Enterococcus raffinosus is one of the Enterococcus species that often cause nosocomial infections. To date, only one E. raffinosus genome has been completely assembled, and the genomic features have not been characterized. Here, we report the complete genome sequence of the strain CX012922, isolated from the feces of a Crohn’s disease patient, and perform a comparative genome analysis to the relevant Enterococcus spp. strains in silico. De novo assembly of the sequencing reads of the strain CX012922 generated a circular genome of 2.83 Mb and a circular megaplasmid of 0.98 Mb. Phylogenomic analysis revealed that the strain CX012922 belonged to the E. raffinosus species. By comparative genome analysis, we found that some strains previously identified as E. raffinosus or E. gilvus should be reclassified as novel species. Genome islands (GIs), virulence factors, and antibiotic genes were found in both the genome and the megaplasmid, although pathogenic genes were mainly encoded in the genome. A large proportion of the genes encoded in the megaplasmid were involved in substrate utilization, such as raffinose metabolism. Giant megaplasmids (~1 Mb) equipped with toxin-antitoxin (TA) systems generally formed symbiosis relationships with the genome of E. raffinosus strains. Enterococcus spp. have a higher species-level diversity than is currently appreciated. The pathogenicity of E. raffinosus is mainly determined by the genome-encoded virulence factors, while the megaplasmid broadens the gene function pool. The symbiosis between the genome and the megaplasmids endows E. raffinosus with large genomic sizes as well as versatile gene functions, especially for their colonization, adaptation, virulence, and pathogenesis in the human gut.

中文翻译：

---

从克罗恩病患者的粪便中分离出的蜡状肠球菌 CX012922 的基因组见解

棉子肠球菌是经常引起医院感染的肠球菌属物种之一。迄今为止，只有一个 E. raffinosus 基因组被完全组装，并且基因组特征尚未被表征。在这里，我们报告了从克罗恩病患者的粪便中分离出来的菌株 CX012922 的完整基因组序列，并对相关的肠球菌属进行了比较基因组分析。硅胶菌株。CX012922 菌株测序读数的从头组装产生了 2.83 Mb 的环状基因组和 0.98 Mb 的环状巨质粒。系统发育分析表明菌株CX012922 属于E. raffinosus 物种。通过比较基因组分析，我们发现一些先前鉴定为 E. raffinosus 或 E. gilvus 的菌株应重新归类为新物种。基因组岛（GIs），尽管致病基因主要在基因组中编码，但在基因组和大质粒中都发现了毒力因子和抗生素基因。大质粒中编码的大部分基因参与底物利用，例如棉子糖代谢。配备毒素-抗毒素 (TA) 系统的巨型巨质粒 (~1 Mb) 通常与 E. raffinosus 菌株的基因组形成共生关系。肠球菌属 具有比目前所认识的更高的物种水平多样性。E. raffinosus 的致病性主要由基因组编码的毒力因子决定，而大质粒拓宽了基因功能库。基因组和大质粒之间的共生赋予 E. raffinosus 大基因组大小以及多功能基因功能，尤其是它们的定植、适应、