Genetic and functional diversity of Streptococcus thermophilus isolated from the Saint-Nectaire cheese-producing PDO area
treptococcus thermophilus is of major importance for cheese manufacturing. Previous studies indicate that the use of commercial strains lead to the loss of typical characteristics of the products. To strengthens the link with the region and improve sensory qualities of cheeses, cheese-producing PDO are increasingly interested for the development of specific autochthonous starter cultures. The present study is therefore focusing on the genetic and functional diversity of Streptococcus thermophilus strains isolated from a local cheese-producing PDO area. Suspected Streptococcus thermophilus isolates were isolated and identified from milk collected on the Saint-Nectaire cheese-producing PDO area and from commercial starters. Whole genome of isolates were sequenced and a comparative analysis based on their pan-genome was carried out. Important functional properties were studied, including acidifying and proteolytic activities. Twenty-two isolates representative of the diversity of the area and four commercial strains were selected. The phylogenetic trees of the 26 isolates does not correspond to the geographic distribution of isolates. The phylogenetic tree resulting from the pan-genome analysis indicates that isolates are divided into 5 distinct groups. A KEGG functional annotation of the accessory genes indicates that the observed diversity comes from the accessory gene content of isolates that are involved in different functional categories. High variability in acidifying activities and little diversity in proteolytic activities were also observed. These results indicate that high genetic and functional variability of the species Streptococcus thermophilus may be isolated from a small (1800km2) appellation area, and may be exploited to meet demand for use as autochthonous starters.