Study On Population Genetics And Functional Genomics Of Lactobacillus Helveticus Isolated From Naturally Fermented Dairy Products

Lactobacillus(L.)helveticus is one of the common lactic acid bacteria in naturally fermented milk as well as an important starter,having been wildely used in the production of fermented dairy products due to its excellent proteolytic activity.The systematic analysis of the genetic background and evolution of L.helveticus is of great significance to the development and utilization of L.helveticus.In this study,the Illumina Hiseq high-throughput sequencing platform was used to complete the whole genome sequencing of 139 strains of L.helveticus isolated from naturally fermented dairy products in China and Mongolia,combined with the whole genome sequence of 41 strains published by NCBI,population genetic and functional genomic studies were conducted and the results obtained are showen as follows:(1)The genetic diversity of L.helveticus was analyzed based on the whole genome data of 180 strains.A core gene set consisting of 708 genes and a pan gene set containing12138 genes were constructed.The phylogenetic analysis based on the core genome divided 180 L.helveticus strains into five evolutionary clades,and their genetic evolution is related with their separated region and source.There are small genetic difference and closer evolutionary distance between the yogurt and kurut clustered strains from Mongolia and China respectively.Yet that of the koumiss clustered strains from Xinjiang of China are farther away from them,and have a greater genetic difference.(2)A total of 49796 single nucleotide polymorphisms(SNPs)were identified,and high-frequency mutation regions mainly occurred in functional gene coding regions.Eleven genes under positive selection pressure were identified common in difference habitat-clustered strains,and their function related to lactic acid production,amino acid transport,carbohydrate metabolism,folate metabolism,cell wall synthesis,and defense mechanisms.There are more genes also under positive selection pressure in koumiss-clustered strains,which related to basic life processes such as carbohydrate metabolism and protein translation,ribosomal structure and biosynthesis.(3)A new cell envelope-associated proteinase PrtH5 was annotated from the 180 L.helveticus genomes.The distribution of cell envelope-associated proteinases of 180 L.Helveticus strains are phylogenetic dependent.The results of amino acid homology analysis demonstrated that PrtH5 and PrtH4 may differentiated from a same ancestor.(4)The association analysis between genome and phenotype showed that the average acid production rate and average proteolysis rate of 60 L.helveticus strains were associated with their phylogeny.The phenotypes between the strains in different clades were significantly different.The averaged acid production rate and average proteolysis rate of the strains positively related with the presence of cell envelope-associated proteinase PrtH3.In conclusion,this study explored the genetic diversity of L.helveticus at the whole genome level and reveals the underlying genetic mechanism of genes related to the proteolytic system of L.helveticus,and the association between the genetic evolution and the fermentation phenotype of the L.helveticus strains by correlating fermentation phenotype,which laid a genetic foundation for the selection of excellent strains.