Comparison of Propionibacterium genomes: CRISPR-Cas systems, phage/plasmid diversity, and insertion sequences

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems constitute the adaptive immune system in prokaryotes that provide resistance against invasive genetic elements. The genus Propionibacterium comprises gram-positive, facultative anaerobe, non-spore-forming bacteria, and is the source of some B group vitamins such as B12 as well as bacteriocins. Some of the selected species of the genus Propionibacterium spp. were reclassified into the three genera in 2016 (Acidipropionibacterium spp., Pseudopropionibacterium spp., Cutibacterium spp.). Therefore, this study compared CRISPR/Cas systems, Cas 1 and repeat sequences phylogeny, phage/plasmid surveys as well as insertion sequences of new genera members. In this study, a total of 34 genomes of 13 species were observed with a bioinformatic approach. CRISPR-Cas +  + and CRISPRDetect were used to detect CRISPR/Cas systems, direct repeats, and spacers. 39 CRISPR-Cas systems were detected. Type I-E, Type I-U, and one incomplete III-B CRISPR-Cas subtypes were identified. Most of the strains had Cas1/Cas4 fusion proteins. Pseudopropionibacterium propionicum strains had two types I-U and one of the CRISPR loci had csx17 cas genes. Common phage invaders were Propionibacterium phage E6, G4, E1, Anatole, and Doucette. The BLSM62 similarity score of all Cas1 sequences was 48.4% while the pairwise identity of repeat sequences was 48.7%. Common insertion sequences were ISL3, IS3, IS30. The diversity analysis of the CRISPR/Cas system in the genus Propionibacterium provided a new perspective for determining the role of the CRISPR-Cas system in the evolution of new genera.