Streptococcus macedonicus and Streptococcus infantarius, two species within the Streptococcus bovis/ Streptococcus equinus complex (SBSEC) are frequently found in spontaneously fermented foods especially of dairy origin. These two species have been suggested to be non-pathogenic and to have been adapted to the dairy environment similarly to Streptococcus thermophilus. Analysis of the first complete genomes of S. macedonicus and S. infantarius indicated that they may be indeed adapted to milk but they also have retained a restricted repertoire of virulence traits when compared to well characterized pathogenic streptococci. In this study we performed comparative genomic analysis among S. macedonicus strains, isolated from Italian, French and Greek dairy products. The contigs of the Italian and French partial genomes were aligned using as a reference the Greek S. macedonicus ACA-DC 198 genome, the only S. macedonicus genome that is completely sequenced to date. Based on these assemblies, we constructed two distinct pseudochromosomes for the French and the Italian strains. Despite the artifactual nature of the two chromosomes, pairwise alignments among the three genomes revealed a high degree of synteny. The genetic information was overall conserved, but strain specific regions also existed. Furthermore, the analysis revealed that the French S. macedonicus strain has lost genes involved in the catabolism of complex plant carbohydrates, in the adhesion to the host’s cells and in haemolysis. On the other hand, an extra lactose operon and a proteolytic system characteristic of lactic acid bacteria were identified, indicating their evolutionary adaptation to the milk environment. Analogous observations could also be made for the Italian strain. Even though our findings further support the adaptation of the S. macedonicus species to milk fermentation, the analysis of the additional S. macedonicus genomes, including non-dairy isolates, may be necessary to clarify its pathogenic potential
