Comparative genomic analysis of the genus Enterococcus.
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.
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. Electronic address: imu150zhongzhi@163.com.
Zhi
Z
Zhong
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. Electronic address: zhangwenyizi@163.com.
Wenyi
W
Zhang
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. Electronic address: 15248195212@163.com.
Yuqin
Y
Song
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. Electronic address: wjliu168@163.com.
Wenjun
W
Liu
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. Electronic address: weiliangxhy@163.com.
Haiyan
H
Xu
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. Electronic address: xixiaoxia22@163.com.
Xiaoxia
X
Xi
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. Electronic address: mhblg@163.com.
Bilige
B
Menghe
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. Electronic address: hepingdd@vip.sina.com.
Heping
H
Zhang
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. Electronic address: sunzhihong78@163.com.
Zhihong
Z
Sun
D000818:Animals; D001089:Arabinose / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D016983:Enterococcus / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006801:Humans; D010802:Phylogeny; D010944:Plants / Q000382:microbiology; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D001089:Arabinose
Comparative genomics; Enterococcus; Evolution; Functional genes; Phylogenetic analysis