Defense systems and prophage detection inStreptococcus mutansstrains

Although the species is extensively studied, limited data are available on antiphage defense systems (APDSs) inStreptococcus mutans. The present study aimed to explore the diversity and the occurrence of APDSs and to search for prophages in the genomes of clinical isolates ofS. mutansusing bioinformatics tools.

Forty-four clinical isolates ofS. mutanswere obtained from saliva samples of people with Parkinson’s disease. Genomic DNA was extracted, sequenced using Illumina MiSeq technology, and analyzed for the presence of defense systems using DefenseFinder. CRISPR- Cas systems were characterized using CRISPRCasFinder, and prophages were detected by the PhiSpy pipeline from RAST. AcrFinder and AcrHub were used to identify anti-CRISPR proteins.

Each strain harbored between 6 and 12 APDS, with restriction-modification systems being the most prevalent, followed by the MazEF toxin-antitoxin system and CRISPR-Cas systems. Type II-C CRISPR-Cas systems were not identified here inS. mutans. Novel variations in type II-A signature protein Cas9 were identified, allowing their classification into four distinct groups. Variability in direct repeat sequences within the same CRISPR array was also observed, and 80% of the spacers were classified as targeting "dark matter". A unique prophage, phi_37bPJ2, was detected, showing high similarity with previously described phages. The AcrIIA5 protein encoded by phi_37bPJ2 was conserved and suggested to remain functionally active.

This study reveals the diversity of APDSs inS. mutansand the limited presence of prophages. The findings provide a foundation for future research on the evolutionary dynamics of these systems and their role inS. mutansadaptation to phage pressure.