Multilocus sequence typing of XXXX from naturally fermented dairy foods in China and Mongolia.

@entity5599 @entity5859 @entity5858 @entity4334 @entity20842
BACKGROUND: @entity5858 is a major dairy starter used for manufacturing of dairy products. In the present study, we developed a @entity5599 ( @entity5599 ) scheme for this important food bacterium. Sequences of 10 housekeeping genes (carB, clpX, dnaA, murC, murE, pepN, pepX, pyrG, recA, and rpoB) were obtained for 239   @entity5859 strains, which were isolated from home-made fermented dairy foods in 18 different regions of Mongolia and China. METHODS: All 10 genes of @entity5859 were sequenced, aligned, and defined sequence types (STs) using the BioNumerics Software. The @entity4334 diversity was calculated by START v2.0. The population structure, phylogenetic relationships and the role of recombination were inferred using ClonalFrame v1.2, SplitsTree 4.0 and Structure v2.3. RESULTS: The 239   @entity5859 isolates and 18 reference strains could be assigned into 119 different STs, which could be further separated into 16 clonal complexes (CCs) and 38 singletons. Among the 10 loci, a total of 132 polymorphic sites were detected. The standardized index of association (I A (S)    =   0.0916), split-decomposition and   /   (relative frequency of occurrence of recombination and mutation) and r/m value (relative impact of recombination and mutation in the diversification) confirms that recombination may have occurred, but it occurred at a low frequency in these 10 loci. Phylogenetic trees indicated that there were five lineages in the @entity5859 isolates used in our study. MSTree and ClonalFrame tree analyses suggest that the evolution of @entity5859 isolates have little relationship with geographic locality, but revealed no association with the types of fermented dairy product. Phylogenetic analysis of 36 whole genome strains (18   @entity5859 , 2   S. vestibularis and 16   @entity20842 strains) indicated that our @entity5599 scheme could clearly separate three closely related species within the salivarius group and is suitable for analyzing the population structure of the other two species in the salivarius group. CONCLUSIONS: Our newly developed @entity5599 scheme improved the understanding on the genetic diversity and population structure of the @entity5859 , as well as provided useful information for further studies on the genotyping and evolutionary research for @entity5859 strains with global diversity.
