Classified as the genospecies Clostridium novyi sensu lato and distributed into four lineages (I–IV), Clostridium botulinum (group III), Clostridium novyi, and Clostridium haemolyticum are clostridial pathogens that cause animal diseases. Clostridium novyi sensu lato contains a large mobilome consisting of plasmids and circular bacteriophages. Here, we explored clustered regularly interspaced short palindromic repeats (CRISPR) arrays and their associated proteins (Cas) to shed light on the link between evolution of CRISPR-Cas systems and the plasmid and phage composition in a study of 58 Clostridium novyi sensu lato genomes. In 55 of these genomes, types I-B (complete or partial), I-D, II-C, III-B, III-D, or V-U CRISPR-Cas systems were detected in chromosomes as well as in mobile genetic elements (MGEs). Type I-B predominated (67.2%) and was the only CRISPR type detected in the Ia, III, and IV genomic lineages. Putative type V-U CRISPR Cas14a genes were detected in two different cases: next to partial type-IB CRISPR loci on the phage encoding the botulinum neurotoxin (BoNT) in lineage Ia and in 12 lineage II genomes, as part of a putative integrative element related to a phage-inducible chromosomal island (PICI). In the putative PICI, Cas14a was associated with CRISPR arrays and restriction modification (RM) systems as part of an accessory locus. This is the first time a PICI containing such locus has been detected in C. botulinum. Mobilome composition and dynamics were also investigated based on the contents of the CRISPR arrays and the study of spacers. A large proportion of identified protospacers (20.2%) originated from Clostridium novyi sensu lato (p1_Cst, p4_BKT015925, p6_Cst, CWou-2020a, p1_BKT015925, and p2_BKT015925), confirming active exchanges within this genospecies and the key importance of specific MGEs in Clostridium novyi sensu lato.

被归类为基因种 新梭状芽孢杆菌 lato 并分为四个谱系 (I–IV)， 肉毒杆菌 （第三组）， 新梭菌， 和 溶血梭菌 是引起动物疾病的梭菌病原体。 新感觉梭菌包含由质粒和环状噬菌体组成的大型移动组。在这里，我们探索了成簇的规则间隔短回文重复序列 (CRISPR) 阵列及其相关蛋白 (Cas)，以阐明 CRISPR-Cas 系统进化与质粒和噬菌体组成之间的联系，该研究对 58新感觉梭菌基因组。在其中 55 个基因组中，在染色体和移动遗传元件 (MGE) 中检测到 IB（完整或部分）、ID、II-C、III-B、III-D 或 VU CRISPR-Cas 系统。IB 型占主导地位 (67.2%)，是在 Ia、III 和 IV 基因组谱系中检测到的唯一 CRISPR 类型。在两种不同的情况下检测到推定的 VU CRISPR Cas14a 型基因：在谱系 Ia 和 12 个谱系 II 基因组中编码肉毒杆菌神经毒素 (BoNT) 的噬菌体上的部分 IB 型 CRISPR 基因座旁边，作为与噬菌体诱导染色体岛（PICI）。在假定的 PCI 中，Cas14a 与 CRISPR 阵列和限制性修饰 (RM) 系统相关，作为辅助基因座的一部分。这是第一次检测到含有此类基因座的 PCI肉毒杆菌. 还根据 CRISPR 阵列的内容和间隔物的研究研究了移动体的组成和动力学。大部分已识别的原型间隔区 (20.2%) 源自新感觉梭菌 （p1_Cst、p4_BKT015925、p6_Cst、CWou-2020a、p1_BKT015925 和 p2_BKT015925），确认了该基因种内的活跃交换以及特定 MGE 在 新感觉梭菌.