Studies On The Genomics And Methylomes Of Streptococcus Thermophilus Isolated From Natural Fermented Dairy Products

As an important bacteria species in natural fermented milk,Streptococcus thermophilus(S.thermophilus)is one of the common leavening used in fermented dairy production and has extensive application prospect and economic value.The fermentation properties of the strain,such as acid production,glycometabolism and protein decomposition capacity are closely related to the quality of fermented milk.Therefore,it is of great significance for the development and utilization of S.thermophilus to analyze the internal relationship between the genotype and phenotype based on the whole genome and methylation information.In the present study,22 representative strains of S.thermophilus with significant differences in acid-producing performance were taken as the research objects.The PacBio SMRT sequencing platform was used to analyze the intrinsic relationship between genotype and phenotype of S.thermophilus at the genomes and methylomes level.The results were shown as follows:(1)The complete genome-wide map of 22 S.thermophilus strains were deciphered,these S.thermophilus genome sequences were highly conserved.However,the genes encoding stress proteins,biosynthesis,and phage related proteins are different among strains.(2)The important functional genes related to acid production,proteolytic ability,carbohydrate active enzyme and CRISPR-Cas system were analyzed by comparative genomics of 22 S.thermophilus.The copy numbers of these interrelated functional genes were little difference among strains,and there was no significant correlation between the copy numbers of acid producing functional genes and acidity values.However,the six strains with the extracellular protease(PrtS)had strong acid-producing ability,all of which belonged to the fast acid-producing group.(3)Two methylation patterns of m6A and m4C were identified in 22 S.thermophilus.The average methylation level of m4C sites was as high as 60%,which is the main methylation modification in S.thermophilus.In addition,2 to 8 motifs of the methylated sites were detected in each strain of S.thermophilus,indicating a high diversity of methylation modification patterns among different strains.(4)Twenty-two S.thermophilus genomes were divided into two groups:fast acid-producing and slow acid-producing,a total of 3130 m4C and 371 m6A differentially methylated genes were identified between the two groups,respectively.These genes are significantly enriched in metabolic pathways such as aminoacyl-tRNA biosynthesis,purine metabolism and terpenoid backbone biosynthesis,of which play an important role in the acid production of S.thermophilus.The possible regulatory mechanism of DNA methylation effect on the acid-producing ability of S.thermophilus is revealed from the perspective of epigenetics.In summary,this study analyzed the correlation between the genotype and phenotype of S.thermophilus based on genomics and methylomes.The whole genomes of 22 S.thermophilus are highly conversed,and the differences were little of key functional genes affecting phenotype characteristics among different strains.Whereas there were differential methylation metabolic pathways between fast acid-producing and slow acid-producing strains,showing DNA methylation was closely related to the phenotypes of S.thermophilus.This study was conductive to analyze the formation mechanism of important acid-producing properties of S.thermophilus,and provided a reference for the resources utilization of S.thermophilus and the development of excellent starter culture.