Comparative genomics of genetic diversity and defense system in Streptococcus thermophilus

Abstract:

[Objective] Streptococcus thermophilus is one of the most commonly used strains in fermented dairy industry. Therefore, it is important to screen S. thermophilus with good fermentation properties. [Methods] The genetic diversity and defense systems of 27 S. thermophilus genomes were analyzed using comparative genomics. [Results] The genetic diversity of S. thermophilus was high based on whole genome analysis. The phylogenetic tree built based on the core genes was divided into two clades, and the strains in Clade 2 were lack of the complete histidine synthesis pathway, thus could not grow normally in the medium lacking histidine. The analysis of defense systems of S. thermophilus reveals the same type of CRISPR locus and restriction modification system was fixed in the genome relatively. The numbers of CRISPR-Cas (P<0.05, r=0.43) and restriction modification systems (P<0.01, r=-0.59) correlated significantly with the number of genes encoding transposases, indicating S. thermophilus has evolved multiple defense systems to protect its genetic integrity by preventing the invasion of exogenous DNA. In addition, the number of CRISPR-Cas system of the Clade 1 strains was significantly (P<0.001) higher than the Clade 2 strains, whereas there was no significant difference in restriction modification systems. These results suggest that the Clade 1 strains had stronger capacity in resistance to phages. [Conclusion] The phylogenetic analysis based on the core genes was divided into two clades. There were some differences in histidine metabolism and defense system between the different clades, providing a new method for the rapid screening of S. thermophilus starters with excellent fermentation characteristics.

Key words:Streptococcus thermophilus;comparative genomics;genetic diversity;CRISPR-Cas system;restriction modification system