Zhong Zhi, Zhang Wenyi, Song Yuqin, Liu Wenjun, Xu Haiyan, Xi Xiaoxia, Menghe Bilige, Zhang Heping, Sun Zhihong
Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Department of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, PR China.
Microbiol Res. 2017 Mar;196:95-105. doi: 10.1016/j.micres.2016.12.009. Epub 2017 Jan 3.
As important lactic acid bacteria, Enterococcus species are widely used in the production of fermented food. However, as some strains of Enterococcus are opportunistic pathogens, their safety has not been generally accepted. In recent years, a large number of new species have been described and classified within the genus Enterococcus, so a better understanding of the genetic relationships and evolution of Enterococcus species is needed. In this study, the genomes of 29 type strains of Enterococcus species were sequenced. In combination with eight complete genome sequences from the Genbank database, the whole genomes of 37 strains of Enterococcus were comparatively analyzed. The average length of Enterococcus genomes was 3.20Mb and the average GC content was 37.99%. The core- and pan- genomes were defined based on the genomes of the 37 strains of Enterococcus. The core-genome contained 605 genes, a large proportion of which were associated with carbohydrate metabolism, protein metabolism, DNA and RNA metabolism. The phylogenetic tree showed that habitat is very important in the evolution of Enterococcus. The genetic relationships were closer in strains that come from similar habitats. According to the topology of the time tree, we found that humans and mammals may be the original hosts of Enterococcus, and then species from humans and mammals made a host-shift to plants, birds, food and other environments. However, it was just an evolutionary scenario, and more data and efforts were needed to prove this postulation. The comparative genomic analysis provided a snapshot of the evolution and genetic diversity of the genus Enterococcus, which paves the way for follow-up studies on its taxonomy and functional genomics.
作为重要的乳酸菌，肠球菌属广泛应用于发酵食品生产。然而，由于一些肠球菌菌株是机会致病菌，其安全性尚未得到普遍认可。近年来，肠球菌属内已描述和分类了大量新物种，因此需要更好地了解肠球菌属物种的遗传关系和进化。在本研究中，对29株肠球菌属模式菌株的基因组进行了测序。结合来自Genbank数据库的8个完整基因组序列，对37株肠球菌的全基因组进行了比较分析。肠球菌基因组的平均长度为3.20Mb，平均GC含量为37.99%。基于37株肠球菌的基因组定义了核心基因组和泛基因组。核心基因组包含605个基因，其中很大一部分与碳水化合物代谢、蛋白质代谢、DNA和RNA代谢相关。系统发育树表明，栖息地在肠球菌的进化中非常重要。来自相似栖息地的菌株间遗传关系更为密切。根据时间树的拓扑结构，我们发现人类和哺乳动物可能是肠球菌的原始宿主，然后来自人类和哺乳动物的物种发生了宿主转移至植物、鸟类、食物和其他环境。然而，这只是一种进化情景，需要更多数据和努力来证实这一假设。比较基因组分析提供了肠球菌属进化和遗传多样性的概况，为其分类学和功能基因组学的后续研究铺平了道路。
