Scaltriti E, Carminati D, Cortimiglia C, Ramoni R, Sørensen K I, Giraffa G, Zago M
Risk Analysis and Genomic Epidemiology Unit, IZSLER, Parma, Italy.
CREA Research Centre for Animal Production and Aquaculture (CREA-ZA), Lodi, Italy.
Lett Appl Microbiol. 2019 May;68(5):394-402. doi: 10.1111/lam.13128. Epub 2019 Mar 21.
Lactobacillus helveticus is a homofermentative thermophilic lactic acid bacteria that is mainly used in the manufacture of Swiss type and long-ripened Italian hard cheeses. In this study, the presence of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) were analysed in 25 L. helveticus genomes and identified in 23 of these genomes. A total of 40 CRISPR loci were identified and classified into five main families based on CRISPR repeats: Ldbu1, Lsal1, Lhel1, Lhel2 and a new repeat family named Lhel3. Spacers had a size between 30 and 40 bp whereas repeats have an average size of 30 bp, with three longer repeats. The analysis displayed the presence of conserved spacers in 23 of the 40 CRISPR loci. A geographical distribution of L. helveticus isolates with similar CRISPR spacer array profiles were not observed. Based on the presence of the signature protein Cas3, all CRISPR loci belonged to Type I. This analysis demonstrated a great CRISPR array variability within L. helveticus, which could be a useful tool for genotypic strain differentiation. A next step will be to understand the possible role of CRISPR/Cas system for the resistance of L. helveticus to phage infection. SIGNIFICANCE AND IMPACT OF THE STUDY: Lactobacillus helveticus, a lactic acid bacteria species widely used as starter culture in the dairy industry has recently also gained importance as health-promoting culture in probiotic and nutraceutical food products. The CRISPR/Cas system, a well-known molecular mechanism that provides adaptive immunity against exogenous genetic elements such as bacteriophages and plasmids in bacteria, was recently found in this species. In this study, we investigated the presence and genetic heterogeneity of CRISPR loci in 25 L. helveticus genomes. The results presented here represent an important step on the way to manage phage resistance, plasmid uptake and genome editing in this species.
瑞士乳杆菌是一种同型发酵嗜热乳酸菌，主要用于生产瑞士型和长时间成熟的意大利硬质奶酪。在本研究中，对25个瑞士乳杆菌基因组中规律成簇间隔短回文重复序列（CRISPR）的存在情况进行了分析，在其中23个基因组中鉴定到了CRISPR。共鉴定出40个CRISPR位点，并根据CRISPR重复序列分为五个主要家族：Ldbu1、Lsal1、Lhel1、Lhel2和一个名为Lhel3的新重复序列家族。间隔序列长度在30至40 bp之间，而重复序列平均长度为30 bp，有三个较长的重复序列。分析显示，40个CRISPR位点中有23个存在保守间隔序列。未观察到具有相似CRISPR间隔序列阵列图谱的瑞士乳杆菌分离株的地理分布情况。基于标志性蛋白Cas3的存在情况，所有CRISPR位点均属于I型。该分析表明瑞士乳杆菌内CRISPR阵列具有很大的变异性，这可能是用于基因型菌株区分的有用工具。下一步将是了解CRISPR/Cas系统对瑞士乳杆菌抵抗噬菌体感染可能发挥的作用。研究的意义和影响：瑞士乳杆菌是一种在乳制品工业中广泛用作发酵剂的乳酸菌，最近在益生菌和营养食品中作为促进健康的培养物也变得越来越重要。CRISPR/Cas系统是一种著名的分子机制，可在细菌中提供针对外源遗传元件（如噬菌体和质粒）的适应性免疫，最近在该物种中被发现。在本研究中，我们调查了25个瑞士乳杆菌基因组中CRISPR位点的存在情况和遗传异质性。此处给出的结果是在该物种中管理噬菌体抗性、质粒摄取和基因组编辑道路上的重要一步。
