Biology subjects

Samot, J.

Publications and source records attributed to Samot, J..

3 recordsLinked to original sources

bioRxiv2025

Structural and genetic diversity of lysis modules in bacteriophages infecting the genus Streptococcus

Bacteriophages infecting the genus Streptococcus play a crucial role in microbial ecology and have potential applications in biotechnology and medicine. Despite their importance, significant gaps remain in our understanding of their lysis modules. This study aims to address these deficiencies by analyzing the genomic diversity and lysis module organization of phages infecting the Streptococcus genus. A search was conducted in the NCBI RefSeq database to identify phage genomes infecting the Streptococcus genus. A representative panel was selected based on taxonomic diversity. Lysis modules were annotated and visualized, functional domains in endolysins were identified, and holins were characterized. A total of 205 phage genomes were retrieved from the NCBI RefSeq database, of which 185 complete genomes were analyzed. A subset of 34 phages was selected for in-depth analysis, ensuring representation of taxonomic diversity. The lysis modules were annotated and visualized, revealing five distinct organizations. Among the 256 identified endolysins, 25 distinct architectural organizations were observed, with amidase activity being the most prevalent. Holins were classified into 9 of the 74 families listed in the Transporter Classification Database, exhibiting 1 to 3 transmembrane domains. This study provides insights into the structural diversity of lysis modules in Streptococcus phages, paving the way for future research and potential biotechnological applications.

microbiology↗

bioRxiv2024

Defense systems and prophage detection in Streptococcus mutans strains

Although the species is extensively studied, limited data are available on antiphage defense systems (APDSs) in Streptococcus 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 of S. mutans using bioinformatics tools. Forty-four clinical isolates of S. mutans were obtained from saliva samples of people with Parkinsons 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 in S. 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 in S. mutans and the limited presence of prophages. The findings provide a foundation for future research on the evolutionary dynamics of these systems and their role in S. mutans adaptation to phage pressure.

microbiology↗

bioRxiv2024

Serotype and distribution of adhesion genes in Streptococcus mutans clinical isolates

The delicate balance of the oral cavity is disrupted by hygiene and diet changes, leading to caries. The virulence of Streptococcus mutans, a key caries pathogen, is partly explained by its rhamnose-glucose polysaccharide (RGP) and its sucrose-dependent and -independent adhesion mechanisms. This study investigates the diversity of S. mutans through analysis of its RGP and the distribution of sucrose-independent adhesion proteins (SpaP, WapA, Cnm, Cbm) in Parkinsons disease patients. In the PARKIDENT clinical trial, strains were isolated from saliva samples of Parkinsons patients before and after oral hygiene procedures. Strains were preanalyzed by multiplex PCR for serotype and collagen-binding proteins, followed by high-throughput sequencing and bioinformatics analysis using RAST(R) and BLAST(R). Phylogenetic analyses and protein modeling were also conducted. Of 40 patients in the Parkident clinical trial, only 24 had Streptococcus mutans strains isolable from salivary swabs. Serotyping revealed that over 80% of the 44 strains isolated were serotype c, in line with prevalence data in the literature. Furthermore, only SpaP types A and B were identified in the strains. The low variability observed for the WapA protein underlines its functional importance. Finally, the cbm gene was not found in any strain, and only 5 strains possessed the cnm gene, all of them serotype c. The study of these 44 Streptococcus mutans strains showed characteristics similar to other populations. Serotype c predominates, with minimal peptide variability in adhesion proteins (SpaP, WapA). Collagen-binding proteins Cnm and Cbm are rare or absent. Further research is essential for detailed strain distribution in Parkinsons-affected and general French populations due to S. mutans growing role in extra-oral pathologies.

microbiology↗