Abstract
BackgroundStreptococcus thermophilus is a major dairy starter used for manufacturing of dairy products. In the present study, we developed a multilocus sequence typing (MLST) 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 S. thermophilus strains, which were isolated from home-made fermented dairy foods in 18 different regions of Mongolia and China.MethodsAll 10 genes of S. thermophilus were sequenced, aligned, and defined sequence types (STs) using the BioNumerics Software. The nucleotide 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.ResultsThe 239 S. thermophilus 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 (IAS = 0.0916), split-decomposition and ρ/θ (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 S. thermophilus isolates used in our study. MSTree and ClonalFrame tree analyses suggest that the evolution of S. thermophilus 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 S. thermophilus, 2 S. vestibularis and 16 S. salivarius strains) indicated that our MLST 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.ConclusionsOur newly developed MLST scheme improved the understanding on the genetic diversity and population structure of the S. thermophilus, as well as provided useful information for further studies on the genotyping and evolutionary research for S. thermophilus strains with global diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0551-0) contains supplementary material, which is available to authorized users.
Highlights
Streptococcus thermophilus is a major dairy starter used for manufacturing of dairy products
The breakdown by region was as follows: 140 strains from 12 different regions of Mongolia were identified as 67 sequence types (STs), and 99 strains from 6 different provinces of China were assigned to 43 STs
A similar distribution was observed for ST65, ST66, and ST91, which were identified in strains isolated from two provinces of China and Mongolia, respectively; the remaining ST strains were isolated in a specific province
Summary
Streptococcus thermophilus is a major dairy starter used for manufacturing of dairy products. We developed a multilocus sequence typing (MLST) 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 S. thermophilus strains, which were isolated from home-made fermented dairy foods in 18 different regions of Mongolia and China. Streptococcus thermophilus is a lactic acid bacteria species that is essential for the manufacturing of many types of fermented dairy products, occurring naturally as well as in commercial starter cultures [1]. Because S. thermophilus can produce large amounts of lactic acid, exopolysaccharides, and flavor compounds in fermentation processes, it is considered the second most important industrial dairy starter after Lactococcus lactis [2, 3]. A powerful method for population genetic studies is multilocus sequence typing (MLST), which is based on sequencing of conserved housekeeping genes. The method provides faster and less expensive nucleotide sequence determination, and has become the gold standard for studying the evolution and population genetics of pathogenic microbes [9]
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