Comparative Genomic Analysis Of The Type Strains Of Genus Enterococcus And Multilocus Sequence Typing Of Enterococcus Faecalis Isolated From Fermented Foods

As a kind of important lactic acid bacteria, Enterococcus is widely used in fermented food. However, as some strains of Enterococcus are opportunistic pathogen, its safety has not been generally accepted, so there are many restrictions in the use of Enterococcus in food industry. At the same time, the comparative genomic analysis of the genus Enterococcus is relatively late. In order to further understand the genetic relationship and the evolution of genus Enterococcus, the comparative genomic analysis was used in this study. The genomes of 29 type strains of Enterococcus were sequenced by the Illumina Miseq high-throughput sequencing platform. In combination with 8 complete genome sequences, the whole genomes of 37 strains of Enterococcus were comparatively analyzed. At the same time, the multilocus sequence typing technology was used to separate four reference strains and the 39 Enterococcus faecalis strains isolated from fermented foods in Inner Mongolia, Qinghai and Tibet. The results were showed as bellow:(1) The whole genomes of 29 type strains of Enterococcus were deciphered. In combination with 8 genomes of Enterococcus, the basic genomic features of all 37 strains were statistically analyzed. The core-genomes which contains 605 genes were defined based on the genomes of the 37 strains of Enterococcus. The core genes were mainly associated with carbohydrate metabolism, protein metabolism, DNA and RNA metabolism.(2) The phylogenetic tree of 37 strains of Enterococcus was constructed based on core-genome sequences and the 37 strains were divided into 8 branches. Six out of 7 strains isolated from plants and birds are in the ancient branches. And all 19 strains isolated from human and mammals distribute in the young branches. At the same time, compared with the old branches, the structure of young branches is more complicated. This may be due to the environment. As human and mammal habitats are more suitable for the evolution of Enterococcus, so the evolution rate is faster in the human and mammal isolates than that in plant and birds isolates, so all the human and mammal isolates were distributed in the young branches.(3) The comparative genomic method was used to study the function of genes in different species. The functional genes related to carbohydrate metabolism, stress response system, virulence factors and antibiotic resistance were discussed detailed.(4) 43 strains of Enterococcus faecalis were divided into 23 sequence types and five clone complexes based on the alleles of five housekeeping gene loci. Correlation analysis of the sequence type and the source showed that the strains isolated from yak milk is relatively concentrated, this may be associated with yak’s unique life habits. We also found that the genetic relationship between four pathogenic strains and dairy isolates are more distant. However, one pathogenic strain Enterococcus faecalis T2 isolated from human urine and 3 strains isolated from sour porridge were distributed in the same clone complex. It suggests us that Enterococcus has to pass strict safety assessment before used in food industry.