Complete Genome Sequencing And Comparative Genomic Analysis Of Pediococcus Acidilactici JQ?-5

Research BackgroundIn recent years,the rapid development of intestinal microbiome has revealed that human health is closely related to intestinal microbes.Probiotics,as one of the means that can interfere with the intestinal microbiome to improve human health,have also attracted much attention.Pediococcus acidilactici is a reliable producer of bacteriocins and is widely used for preservation and safety assurance during food storage.In addition,the probiotic functions of P.acidilactici have also received widespread attention,such as regulating intestinal immunity,lowering cholesterol and triglycerides and so on.Although it has broad application prospects,it is difficult to correctly evaluate and use the efficacy of probiotic products containing P.acidilactici in the market due to the different functions that different P.acidilactici strains may have.A comprehensive analysis of the genome,genetic characteristics and potential functions of this species is the premise for the accurate development and rational use of the probiotic products of P.acidilactici.Research Methods1.The whole genome of P.acidilactici JQ?-5 was sequenced on Pacbio RS? and Illumina Hiseq platforms,respectively.The information of completion map was obtained through genome assembly,and the gene prediction and annotation were completed to understand its genome characteristics,and its safety and probiotic characteristics were evaluated at the genome level.2.A pan-genomic analysis,phylogenetic analysis,bacteriocin coding gene mining,carbohydrate metabolic capacity prediction and mobile genetic element analysis including CRISPR/Cas system were performed on 41 strains of P.acidilactici,including P.acidilactici JQ?-5.Research Results1.Through whole genome sequencing and splicing,the complete genome sequence of P.acidilactici JQ?-5(Genbank accession number: CP023654)was obtained.The genome of P.acidilactici JQ?-5 consists of a complete circular chromosome of 2,085,679 bp,with an average GC content of 42.16% and encoding2035 genes.The genome contains 5 sets of 16s-23s-5s ribosomal RNA operons and 56 transfer RNAs.2.P.acidilactici JQ?-5 contains 1 complete prophage,6 gene island fragments,1extracellular polysaccharide gene cluster,and does not contain virulence genes,antibiotic resistance genes and secondary metabolite synthesis genes.3.Pan-genome analysis showed that the pan-genome of P.acidilactici showed an open trend,and the pan-genome contained 75% of non-essential genes.4.In the evolutionary analysis of P.acidilactici,the average nucleotide identity between the two genomes was greater than 96%.All the strains in the phylogenetic tree were different from the functional genome distribution tree except the five strains in group G.5.Three kinds of bacteriocins were found in 41 strains of P.acidilactici,namely pediococcin PA-1,enterolysin A and colicin-B.The genes encoding enterolysin A and colicin-B are homologous to phage and plasmid genes,respectively.6.In carbohydrate metabolism analysis,most P.acidilactici can metabolize plant polysaccharides and lactose.7.Many strains of P.acidilactici contain different proportions of exogenous genes involved in the construction of a variety of mobile genetic elements,including transposable elements,plasmids and prophages.For mobile genetic elements,the ?-A CRISPR/Cas locus was found in the genomes of 32 strains of P.acidilactici,and the DR sequence in the CRISPR locus belonged to the Lsal1 family and was highly conserved.Research Conclusions1.P.acidilactici JQ?-5 has stable genome and high safety,and has the potential to resist extreme environment.It can be used as probiotics and starter culture in the food industry.2.P.acidilactici species have high genetic diversity and can continuously communicate with the external environment to adapt to the harsh environment.3.Although many P.acidilactici genomes have similar gene contents,their collinearity is low,suggesting that a large number of gene rearrangement events occurred in the P.acidilactici genomes.4.Functional gene differences of P.acidilactici were mainly reflected in bacteriocin production,carbohydrate utilization,horizontal gene transfer related genes(CRISPR/Cas and mobile genetic elements).5.HGT event is an important driving force for the evolution of P.acidilactici,and it may have acquired the ability to produce enterolysin A and colicin-B from other species through HGT events.This provides a new perspective for studying the evolutionary relationships between species.6.Most P.acidilactici can ferment plant polysaccharides and lactose,and can be used as intestinal probiotic supplements and dairy starter.