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Here is presented the whole-genome sequences of Streptococcus thermophilus strains MTH17CL396 and M17PTZA496, isolated from fontina protected designation of origin (PDO) cheese in the Valle d'Aosta Region (Italy). S. thermophilus is a lactic acid bacterium widely present in dairy products, and these are the first publicly available genome sequences of S. thermophilus strains isolated from cheese.

Genome Sequences of Streptococcus thermophilus Strains MTH17CL396 and M17PTZA496 from Fontina, an Italian PDO Cheese