Population Genetics And Functional Genomics Of Streptococcus Thermophilus Isolated From Natural Fermented Dairy Products

Streptococcus(S.)thermophilus,with a long history of application in fermented milk,is one of the most important bacteria in natural fermented milk.Because of its excellent fermentation characteristics,S.thermophilus is widely used as starter in the production of fermented dairy products.Genetic evolution is the primary basis for the research and development of industrial strains,while the study of genetic evolution of S.thermophilus population hasn't been done at present.Thus,the study of genetic variation and evolution of S.thermophilus has a great significance to the exploitation and utilization of S.thermophilus strains.In present study,the whole genomes of 185 S.thermophilus strains,isolated from natural fermented dairy milk in China and Mongolia,were deciphered by whole-genome resequencing technology to further determine the genetic evolution of S.thermophilus population.Besides,the functional genomics of S.thermophilus was studied by genomewide association studies.The results were shown as follows:(1)The whole genomes of 185 S.thermophilus strains were deciphered.And the coreand pan-genome of S.thermophilus were constructed.(2)The results of genetic variation analysis showed that high mutation rate mainly occurred in pseudogenes and intergenic region of S.thermophilus genomes.The genetic diversity of kurut isolates and yoghurt isolates were higher than other isolates.(3)The results of genetic evolution demonstrated that there was a direct relationship between S.thermophilus isolates and their isolation location and origin.Depending on the genetic distance to the most recent common ancestor,the nich shift of S.thermophilus may be from Tibet,Qinghai to Mongolia(Tov Province,Orkhon Province),Xinjiang,Inner Mongolia,Sichuan,Gansu to Mongolia(Zavkhan province,Khovsgol province,Sukhbaatar province)again.(4)The functional genes related to the phenotypic characteristics of S.thermophilus were identified by genome-wide association studies.The genes related to the acidogenic ability of S.thermophilus were mainly those functional genes involved in sugar metabolism,amino acid hydrolysis,detoxification,and dairy flavor.The genes related to altitude included cold stress protein coding genes and genes involved in carbohydrate,protein and lipid metabolism.In addition,the multivariate regression model based on the principle of GWAS can predict the acidogenic ability of S.thermophilus,thus provide an efficient method for S.thermophilus screening.(5)Important functional genes of 185 S.thermophilus strains related to fermentation characteristics and resistance to environmental stress were obtained,which provides a theoretical basis for the development and utilization of S.thermophilus strains.In conclusion,this study revealed the genetic diversity and evolution of S.thermophilus in natural fermented dairy products at a genomic level.The functional genes related to the phenotypic characteristics of S.thermophilus were analyzed by the genome-wide association analysis.Plus,an efficient method of bacteria screening was established.This study provides a theoretical basis for the development and utilization of S.thermophilus strains.