Dairy streptococcal cell wall and exopolysaccharide genome diversity

Abstract

The large-scale and high-intensity application of Streptococcus thermophilus species in milk fermentation processes is associated with a persistent threat of (bacterio)phage infection. Phage infection of starter cultures may cause inconsistent, slow or even failed fermentations with consequent diminished product quality and/or output. The phage life cycle commences with the recognition of, and binding to, a specific host-encoded and surface-exposed receptor, which in the case of S. thermophilus can be the rhamnose-glucose polysaccharide (RGP; specified by the rgp gene cluster) or exopolysaccharide (EPS; specified by the eps gene cluster). The genomic diversity of 23 S . thermophilus strains isolated from unpasteurized dairy products was evaluated, including a detailed analysis of the rgp and eps loci. In the present study, five novel eps genotypes were identified while variations of currently recognized rgp gene cluster types were also observed. Furthermore, the diversity of rgp genotypes amongst retrieved isolates positively correlated with phage diversity based on phageome analysis of eight representative dairy products. Our findings therefore substantially expand our knowledge on S. thermophilus’ strain and phage diversity in (artisanal) dairy products and highlight the merit of phageome analysis of artisanal and traditional fermented foods as a sensitive marker of dominant microbiota involved in the fermentation.

Keywords: EPS; RGP; Streptococcus thermophilus; bacteriophage; exopolysaccharides; phageome; rhamnose-glucose polysaccharides.

Fig. 1.

Schematic overview of the organization and sequence relatedness the RGP-specifying gene clusters of S. thermophilus strains (A–E), including five reference strains of S. thermophilus (*) for each respective RGP type. Regions of homology (% amino acid identity) are joined by blocks of different shades of grey to black as indicated in the figure. The proposed functions of the individual protein-encoding regions are colour coded and indicated within the figure. Scale bar was measured in base pair (bp). † indicates where representative examples of identical gene clusters are presented; the RGP-encoding operons of Moz111, Moz76, Brie16, FDL19 and Rico66 are identical to SMQ-301 and Moz83.

Fig. 2.

Schematic overview of the organization and sequence relatedness the EPS-specifying gene clusters of S. thermophilus strains (type A to J), including five reference strains of S. thermophilus (*). Regions of homology (% amino acid identity) are joined by blocks of different shades of grey to black as indicated in the schematic. The proposed functions of the individual protein-encoding regions are colour coded and indicated above the figure. Scale bar is measured in base pair (bp). In the case where the eps cluster was retrieved from different contigs, break symbol (//) was used.

Fig. 3.

Relative % of read mapping to streptococcal phage (cos, pac, 5093, 987) distribution in eight cheese samples – brie, mozzarella B (moz), ricotta (rico), stracciatella (strac), vacherin (vach), semi-soft cheese D (ssc D), semi-soft cheese A (ssc A) and blue cheese, based on phageome analysis.