Study On Population Genetics And Functional Genomics Of Limosilactobacillus Fermentum

L.fermentum has been used in industrial production and food fermentation for a long time and has been identified as a recognized safe LAB.It has been prove to have probiotic effects such as prevent pathogenic bacteria infection and increasing the immunity of body.At present,most of the studies on L.fermentum mainly focus on phenotypic traits and probiotic properties.There are few studies on genetic background and functional genes characteristics of this species.It is of great significance for its basic research and industrial application to analyze the genetic diversity and functional genes characteristics of L.fermentum from the genome level.In this study,73 strains of L.fermentum were provided by Lactic Acid Bacteria Collection Center of Inner Mongolia Agricultural University,and their whole genomes were resequenced using Illumina Novaseq high-throughput sequencing platform.Combined with the whole genome sequence of 90 strains of L.fermentum published in NCBI Ref Seq database,the population genetics and functional genomics of 163 strains of L.fermentum were analyzed.The results were shown as follows:(1)The genomic size of 163 strains of L.fermentum were 1.92±0.17 Mb and GC content were 51.96±0.44%.There were significant differences in genomic size and GC content among different isolate sources.The human-derived strains have larger genome size and lower GC content(P<0.05),while the milk-derived strain is different.(2)449 core-genes and 12,776 pan-genes of 163 strains of L.fermentum were constructed.The genome of this species was an open genome.The main functions of core-genes are protein translation,carbohydrate metabolism and nucleotide metabolism.(3)A phylogenetic tree of 163 strains of L.fermentum was constructed based on 449core-genes.The strains divided into four evolutionary clades.The isolates source separation is the main factor affecting the evolution of L.fermentum.It likely caused by is genetic variation of the species when it evolved to a nutrient-rich environment.(4)A total of 82,094 SNP sites.9,438 were located in the intergenic region and 72,656 in the coding region using L.fermentum F6 as the reference sequence.The results of recombination analysis showed that there was recombination in L.fermentum species,but the degree was low.(5)Functional genomics analysis showed that there were significant differences in functional genes among different isolates.The plant-derived strain possesses the characteristic xylanesterase,which is involved in cellulose degradation.The milk-derived strain had more β-galactosidase,which was related to its adaptation to the milk environment.At the same time,the milk-derived strain had more Spacers and Cas proteins.The results showed that the strain had certain habitat adaptability in order to adapt to different habitats.In summary,this study explored the genetic diversity of L.fermentum at the genomic level.The potential genetic rules were revealed,and exploration the functional genes difference among different isolated strains.This study provides a theoretical basis for the research and development of L.fermentum genome.