Within the Streptococcus genus, only Streptococcus thermophilus is considered to be non-pathogenic due to its adaptation to the milk environment. Streptococcus macedonicus is also an intriguing streptococcal species since its most frequent source of isolation to date is fermented foods, mainly of dairy origin. Sequencing of S. macedonicus ACA-DC 198 genome was performed using a combination of 454 GS FLX pyrosequencing and HiSeq 2000 Illumina sequencing. The hybrid assembly between 454 and HiSeq2000 data (>200x coverage) resulted in one continuous genomic scaffold of 2,130,034 bp and a plasmid of 12,728 bp. The genome assembly was validated against a NheI optical map of the S. macedonicus genome. Sequences were annotated with the BaSys and the RAST pipelines and manually curated using Kodon. Final corrections were made based on the quality assessment of the annotation using GenePRIMP. We found 2,192 protein-coding genes on the chromosome, 192 of which were identified as potential pseudogenes, indicating an ongoing genome decay process. This hypothesis is also supported by the approximately 220 kb-smaller genome size of S. macedonicus compared to the S. gallolyticus genomes, despite the high level of gene synteny between the two species. Such a reductive evolutionary process is common for lactic acid bacteria domesticated to the food environment, which in the case of S. thermophilus was also accompanied by the loss of pathogenicity traits. With our in silico analysis we attempt to investigate whether S. macedonicus shows traits that would support its adaptation to the dairy environment at the genomic level.
