Study On Population Genetics And Functional Genomics Of Lactobacillus Delbrueckii Subsp. Bulgaricus

Lactobacillus(L.)delbrueckii subsp.bulgaricus,the model species of Lactobacillus,is one of the most commonly used starter strains for industrial production of fermented dairy products.The production performance of the strain,such as protein decomposition activity,lactose metabolism ability and post-acidification characteristics,do affect the quality and characteristics of fermented dairy products.It would generate great economic significance to screen and develop starter strains with excellent performance.Natural fermented dairy products contain abundant lactic acid bacteria resources,which have a wide range of phenotypic and genetic diversity that lead to varied fermentation characteristics among different strains.However,the related research in this field is rarely reported.Therefore,the systematic analysis of the genetic background and evolution of L.delbrueckii subsp bulgaricus would largely improve the development and utilization of lactic acid bacteria resources.In this study,200 strains of L.delbrueckii subsp bulgaricus were selected for population genetics and functional genomics studies,and the following conclusions were obtained.(1)The genetic diversity and population structure of L.delbrueckii subsp bulgaricus were studied for the first time at the whole genome level.A total of 44559 SNPs and 7271 InDels were identified.A core gene set of 1087 genes and a pan-gene set of 3436 genes were constructed.Further phylogenetic analysis divided L.delbrueckii subsp bulgaricus into four branches.The results of population genetic analysis showed that the L.delbrueckii subsp bulgaricus population had very high genetic diversity and recombination heterogeneity.Recombination and natural selection served as its driving force for evolution of the L.delbrueckii subsp bulgaricus populations.(2)Combined with the phenotypic characteristics of curd time,acid producing rate,proteolytic ability and glycometabolism capacity of 25 representative strains,from the aspect of functional genomics,genome-wide association study was performed,and a nonsynonymous SNP site that significantly associated with the acid production property of the strain was identified.The site was located in Ldb2036,a homologous gene of lactate dehydrogenase.It was proved that the accuracy of this locus could be over 80%,and could be potentially used to rapidly screen for strains with improved capability on acid production.(3)PacBio SMRT sequencing technique was used to complete the genomic analysis and methylation analysis of 9 strains.The m6 A and m4 C methylation patterns and 37 motifs of the methylated sites were identified.This was the first time to constructed methylation sites map for Lactobacillus delbrueckii subsp.bulgaricus.We revealed the mechanism of the difference in the fermentation characteristics among strains in perspective of epigenetics.This study explored the genetic diversity of Lactobacillus delbrueckii subsp.bulgaricus from the whole genome level and revealed the underlying evolutionary mechanism of whole population and the functional genes.It lays a theoretical foundation for further development and utilization of lactic acid bacteria in industry,which has important guiding significance for actual production.