Novel Genus of Phages Infecting Streptococcus thermophilus: Genomic and Morphological Characterization

Streptococcus thermophilus is a lactic acid bacterium commonly used for the manufacture of yogurt and specialty cheeses. Virulent phages represent a major risk for milk fermentation processes worldwide as they can inactivate the added starter bacterial cells, leading to low quality fermented dairy products. To date, four genetically distinct groups of phages infecting S. thermophilus have been described. Here, we describe a fifth group. Phages P738 and D4446 are virulent siphophages that infect a few industrial strains of S. thermophilus The genomes of phages P738 and D4446 were sequenced and found to contain 34,037 and 33,656 base pairs (bp) as well as 48 and 46 open reading frames, respectively. Comparative genomic analyses revealed that the two phages are highly related to each other but display very limited similarities to other S. thermophilus phages. In fact, these two novel S. thermophilus phages share similarities with streptococcal phages of non-dairy origin, suggesting that they emerged recently in the dairy environment.Importance Despite decades of research and adapted anti-phage strategies such as CRISPR-Cas systems, virulent phages are still a persistent risk for the milk fermentation industry worldwide as they can cause manufacture failures and alter product quality. Phages P738 and D4446 are novel virulent phages that infect the food-grade Gram-positive bacterial species Streptococcus thermophilus These two related viruses represent a fifth group of S. thermophilus phages as they are significantly distinct from other known S. thermophilus phages. Both phages share similarities with phages infecting pathogenic streptococci, suggesting their recent emergence and probable co-existence in dairy environments. These findings highlight the necessity of phage surveillance programs as the viral population evolves in response to the application of anti-phage strategies.