Genetic and phenotypic diversity of Streptococcus spp. strains isolated from a low-moisture Mozzarella production site

Streptococcus thermophilus is a lactic acid bacterium (LAB) used as starter cultures (starters) in fermentations in the dairy industry. However, non-starter wild type (WT) S. thermophilus can survive thermal treatments, produce biofilm and hence colonize dairies to contaminate processing lines and final products, including cheese whey which is later used for various high-value ingredients.

This study aims to explore key genomic differences between S. thermophilus starters and WTs and map the diversity of WT strains in a cheese plant. Furthermore, phenotypical characteristics of dairy isolates, such as heat resistance and biofilm formation were investigated.

In this work, we analysed organic and conventional milk samples (total sampling rounds n=6) after heat treatment from different locations (n=7) in a cheese plant. Streptococcus spp. strains were identified by MALDI-TOF MS and the genomes of 136 representative isolates sequenced. Biofilm formation capacity of relevant strains was evaluated through safranin staining and heat resistance experiments were performed in skim milk.

Results show that Streptococcus spp. were present in 57% of the samples. According to whole genome phylogeny and average nucleotide identity, most Streptococcus spp. strains could be grouped into four major clusters. Twelve presumed WT strains had between 150-200 single nucleotide polymorphism differences compared to known starters, which may suggest starters at some point have adapted to the dairy environment. Knowledge of genotypes, and phenotypic diversity will be used to design of a detection method and mitigative strategies for control of WT Streptococcus spp. to ensure product quality.