Isolation,Comparative Genomics And Safety Assessment Of Lactobacillus Gasseri And Lactobacillus Paragasseri

Lactobacillus gasseri is one of the important species in gastrointestinal tract and vaginal tract.As its probiotic characteristics,some strains have been used in food industry.Howere,the comparative genomics was conducted.In 2008,through whole-genome sequence analyses and bioinformatics analysis,Lactobacillus paragasseri was divided from L.gasseri and become a new species.The differences between the two species at the genetic level are unclear.Therefore,based on comparative genomics to clarify the similarities and differences between the two species is of great significance for selection and development of L.gasseri and L.paragseeri.In this study,strains were isolated from human feces and vaginal samples.Illumina Hiseq high-throughput sequencing was used to complete the genome of them.The genomic analysis was carried out to study evolutionary relationship of each strains as well as distinguish species,including comparative genomics and pan-genomes.In addition,the prophage,virulence and drug resistance genes in the two species were predicted,and resistance to 13 common antibiotics were tested to evaluate the safety of the strains.The main results are as follows:(1)Strains were isolated from human feces and vaginal samples identified by strain-specific primers GroEL,130 strains of “L.gasseri” were obtained.After sequencing draft genome,“L.gasseri” was initially divided into two groups with ANI threshold of 96%,one group contained 105 strains with ANI range 97.89% to 99.92%,the other group was consisted of 25 strains with ANI ranged from 93.26% to 94.08%.Phylogenetic based on orthologous and housekeeping analysis confirmed that 105 of them were L.paragasseri and other 25 strains were L.gasseri.(2)In order to analyze the composition and characteristics of L.gasseri and L.paragasseri,the pan-genome and core-genome were calculated separately.The L.paragasseri had an open pan-genome containing 7371 genes and core-genome containing 1274 genes.L.gasseri had a close pan-genome containing 3614 genes and core-genome containing 1360 genes.(3)To further compare the genomic differences between L.gasseri and L.paragasseri,genes related to carbohydrate active enzymes,bacteriocins and CRISPR-Cas system of two the species were analyzed.The results showed that the carbohydrate active enzyme family GH42 was only present in L.paragasseri.Various bacteriocin operons were predicted in L.paragasseri.And only one or two bacteriocin operons were predicted in L.gasseri.The L.gasseri contained type IE and IIA CRISPR-Cas system,and some L.paragasseri only had type IIA CRISPR-Cas system.These different genes were the reason for clustering of the two species,and high intraspecific diversity in L.gasseri and L.paragasseri.(4)The safety of L.paragasseri and L.gasseri at genetic level were evaluated by analyzing the presence of prophage,virulence and drug resistance genes.Intact prophage sequence was identified in 76 strains out of 130 strains,44 drug resistance genes and 21 virulence related genes involved in adhesion,anti-phagocytosis and invasion were detected inall strains.The MIC of 13 antibiotics showed that all of the strains had different resistance to different antibiotics.