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.

分类为诺维梭菌基因种，分为四个谱系（I-IV），肉毒梭菌（III组）、诺维梭菌和溶血梭菌是引起动物疾病的梭菌病原体。新梭菌含有一个由质粒和环形噬菌体组成的大型移动组。在这里，我们在对 58 个新梭菌基因组的研究中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 系统的进化与质粒和噬菌体组成之间的联系。 。在其中 55 个基因组中，在染色体以及移动遗传元件 (MGE) 中检测到 IB 型（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%)，并且是在 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 型 CRISPR Cas14a 基因：紧邻 Ia 谱系和 12 个 II 谱系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 位点，作为与噬菌体诱导的染色体岛（PICI）。在假定的 PICI 中，Cas14a 作为辅助基因座的一部分与 CRISPR 阵列和限制性修饰 (RM) 系统相关。这是首次在肉毒梭菌中检测到含有此类基因座的 PICI。还根据 CRISPR 阵列的内容和间隔区的研究，研究了移动组的组成和动力学。大部分已识别的原型间隔子（20.2%）源自新梭菌（p1_Cst、p4_BKT015925、p6_Cst、CWou-2020a、p1_BKT015925 和 p2_BKT015925），证实了该基因种内的活跃交换以及新梭菌中特定 MGE 的关键重要性。