Genome Analysis and Physiological Characterization of Four Streptococcus thermophilus Strains Isolated From Chinese Traditional Fermented Milk

Abstract

Streptococcus thermophilus plays important roles in the dairy industry and is widely used as a dairy starter in the production of fermented dairy products. The genomes of S. thermophilus strains CS5, CS9, CS18, and CS20 from fermented milk in China were sequenced and used for biodiversity analysis. In the present study, the phylogenetic analysis of all 34 S. thermophilus genomes publicly available including these four strains reveals that the phylogenetic reconstruction does not match geographic distribution as strains isolated from the same continent are not even clustered on the nearby branches. The core and variable genes were also identified, which vary among strains from 0 to 202. CS9 strain contained 127 unique genes from a variety of distantly related species. It was speculated that CS9 had undergone horizontal gene transfer (HGT) during the long evolutionary process. The safety evaluation of these four strains indicated that none of them contains antibiotic resistance genes and that they are all sensitive to multiple antibiotics. In addition, the strains do not contain any pathogenic virulence factors or plasmids and thus can be considered safe. Furthermore, these strains were investigated in terms of their technological properties including milk acidification, exopolysaccharide (EPS) and γ-aminobutyric acid (GABA) production, and in vitro survival capacity in the gastrointestinal tract. CS9 possesses a special eps gene cluster containing significant traces of HGT, while the eps gene clusters of CS5, CS18, and CS20 are almost the same. The monosaccharide compositional analysis indicated that crude EPS-CS5, EPS-CS9, EPS-CS18, and EPS-CS20 contain similar monosaccharide compositions with different ratios. Furthermore, CS9 was one of a few GABA-producing strains that could ferment glutamate to produce GABA, which is beneficial for improving the acid tolerance of the strain. CS18 has the most potential for the production of fermented food among these four strains because of its fast growth rate, rapid acidifying capacity, and stronger acid and bile salt resistance capacity. This study focused on the genome analysis of the four new S. thermophilus strains to investigate the diversity of strains and provides a reference for selecting excellent strains by use of the genome data.

Comparative transcriptome analysis for the biosynthesis of antioxidant exopolysaccharide in Streptococcus thermophilusCS6

“…Mostly either permeases or PEP-PTS systems are responsible for transporting various monosaccharides and disaccharides in S. thermophilus. 16 Environmental conditions could influence the expression of sugar transportation-related genes in LAB. In S. thermophilus MN-ZLW-002, lacS was highly expressed in the mid-exponential, late-exponential and stationary phases compared with the late-lag phase.…”

“…31 Furthermore, activation of N-acetyl-glucosamine and N-acetyl-muramic acid is also observed in cell wall metabolism by multiple enzymes. 16 In the process of sugar activation, differentially-regulated metabolism in CS6 comprised galactose metabolism and cell wall metabolism. Both nutrition (carbon and nitrogen sources) and environmental stress (pH) regulate nucleotide sugar formation in other LABs.…”

“…Determination of monosaccharide composition was performed as described by Hu et al 16 but with slight modifications. For this, 4 mg of crude EPS was mixed in 4 mol L −1 CF 3 COOH to hydrolyze at 110 °C for 3 h, with a further drying procedure at a nitrogen flow.…”

Dairy streptococcal cell wall and exopolysaccharide genome diversity

“…The CRISPR spacer array profiles can be used as unique identifiers of distinct strains [31,32]. A number of studies have highlighted the presence of dairy streptococci in artisanal fermented foods from a range of geographical locations through metagenomic and/or microbiological approaches [33][34][35][36][37]. Isolates have been characterized largely based on technologically relevant properties including EPS production and structural characteristics [37], antibiotic sensitivity, milk acidification ability and/or gelling capabilities [34].…”

“…A number of studies have highlighted the presence of dairy streptococci in artisanal fermented foods from a range of geographical locations through metagenomic and/or microbiological approaches [33][34][35][36][37]. Isolates have been characterized largely based on technologically relevant properties including EPS production and structural characteristics [37], antibiotic sensitivity, milk acidification ability and/or gelling capabilities [34]. Within an individual product, it can be challenging to assess if more than one strain of S. thermophilus is present due to high levels of sequence conservation across the genomes of strains of this species.…”