Comparative Genomic Research Of Enterococcus Faecium Isolated From Different Habitats

As a lactic acid bacteria,application of Enterococcus faecium(E.faecium)in food fermentation has been controversial,this is mainly due to the fact that some E.faecium are opportunities bacteria and are resistant to a variety of antibiotics.In this research,54 strains of E.faecium isolated from naturally fermented dairy products were sequenced by Illumina MiSeq high-throughput sequencing technology.At the same time,107 genomes of E.faecium with clear source were downloaded from NCBI database.The comparative genome analysis of 161 strains of E.faecium was carried out.To study the evolutionary relationship between dairy isolates and animal gastrointestinal tract isolates,human gastrointestinal tract isolates,human blood isolates and other environmental isolates,environmental specific genes,drug resistance genes,virulence genes and pre-phages,and then to evaluate the safety of E.faecium in natural fermented dairy products.The main results are as follows:1.The average genome size of E.faecium·was 2.85±0.20 Mb,the GC content was 37.97±0.22%and the predicted number of genes was 2,765±187.Human isolates had the largest genome and the largest number of predicted genes,which were significantly higher than those of other environmental isolates.2.The pan-genomes of the 161 E.faecium strains was composed of 12,457 gene families,and the core gene set contained 1,013 genes.The functional classification of these genes revealed that genes involved in carbohydrate,amino acid and nucleotide transport and metabolism accounted for a large proportion in the core genome.3.The phylogenetic trees of 161 strains of E.faecium was constructed by core genome.There was a correlation between the isolated source and phylogeny.The results showed that the natural environment played an important role in the genome formation of E.faecium.4.The amino acid sequences of 161 strains of E.faecium were compared with the drug resistance gene database by BLAST,and a total of 41 drug resistance genes were found.The average number of drug resistance genes per strain of dairy isolates was 5.3,which was significantly lower than that of other environmental isolates.5.The genomes of 161 strains of E.faecium was compared with the virulence factor database,a total of 13 virulence genes were found,with an average of 4.9 species per strain.It is mainly an adhesion protein that mediates adhesion to host tissue.In addition,the number of virulence factors of dairy isolates was significantly lower than that of other environmental isolates.6.According to our definition of environment-specific genes,202 environment-specific genes were identified,including 136 dairy product-specific,31 human blood-specific and 35 human gastrointestinal tract-specific genes.The results shows that E.faecium has highly genomic plasticity.Comparative genomics research showed that the genomes of E.fciecium were significant differences between dairy isolates and other environmental isolates,but there were still many drug resistance genes and virulence factors.Therefore,there is a risk in the application of dairy isolates of E.faecium in food,and its safety should be further evaluated.