Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, S7N 5B4, Canada.
Microb Ecol. 2013 Jul;66(1):182-8. doi: 10.1007/s00248-013-0217-0. Epub 2013 Mar 28.
Clustered regularly interspaced short palindromic repeats (CRISPR) are currently a topic of interest in microbiology due to their role as a prokaryotic immune system. Investigations of CRISPR distribution and characterization to date have focused on pathogenic bacteria, while less is known about CRISPR in commensal bacteria, where they may have a significant role in the ecology of the microbiota of humans and other animals, and act as a recorder of interactions between bacteria and viruses. A combination of PCR and sequencing was used to determine prevalence and distribution of CRISPR arrays in Enterococcus faecalis and Enterococcus hirae isolates from the feces of healthy pigs. Both type II CRISPR-Cas and Orphan CRISPR (without Cas genes) were detected in the 195 isolates examined. CRISPR-Cas was detected in 52 (46/88) and 42 % (45/107) E. faecalis and E. hirae isolates, respectively. The prevalence of Orphan CRISPR arrays was higher in E. faecalis isolates (95 %, 84/88) compared with E. hirae isolates (49 %, 53/107). Species-specific repeat sequences were identified in Orphan CRISPR arrays, and 42 unique spacer sequences were identified. Only two spacers matched previously characterized pig virome sequences, and many were apparently derived from chromosomal sequences of enterococci. Surprisingly, 17 (40 %) of the spacers were detected in both species. Shared spacer sequences are evidence of a lack of species specificity in the agents and mechanisms responsible for integration of spacers, and the abundance of spacer sequences corresponding to bacterial chromosomal sequences reflects interspecific interactions within the intestinal microbiota.
成簇规律间隔短回文重复序列（CRISPR）目前在微生物学领域是一个研究热点，因为它们作为原核生物的免疫系统发挥着作用。迄今为止，对 CRISPR 分布和特征的研究主要集中在致病菌上，而对共生菌中的 CRISPR 了解较少，在那里它们可能在人类和其他动物微生物群的生态学中发挥重要作用，并作为细菌和病毒相互作用的记录者。我们采用聚合酶链反应（PCR）和测序相结合的方法，检测了来自健康猪粪便中的粪肠球菌和屎肠球菌分离株中 CRISPR 基因簇的分布和特征。在 195 个分离株中检测到了 II 型 CRISPR-Cas 和孤儿 CRISPR（无 Cas 基因）。在 88 个粪肠球菌和 107 个屎肠球菌分离株中分别检测到了 CRISPR-Cas 基因，其检出率分别为 52%（46/88）和 42%（45/107）。与屎肠球菌分离株（49%，53/107）相比，粪肠球菌分离株中孤儿 CRISPR 基因簇的检出率更高（95%，84/88）。在孤儿 CRISPR 基因簇中鉴定到了种特异性重复序列，共鉴定到 42 个独特的间隔序列。只有两个间隔序列与先前表征的猪病毒组序列匹配，许多间隔序列显然来自肠球菌的染色体序列。令人惊讶的是，在两个种中均检测到了 17 个（40%）间隔序列。共享间隔序列表明负责间隔序列整合的因子和机制缺乏种特异性，与细菌染色体序列相对应的间隔序列的丰度反映了肠道微生物群内的种间相互作用。
