Shin Hanseob, Kim Yongjin, Unno Tatsuya, Hur Hor-Gil
School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju, Republic of Korea.
Microbiol Spectr. 2023 Jan 31;11(2):e0493422. doi: 10.1128/spectrum.04934-22.
The clustered regularly interspaced short palindromic repeat (CRISPR) has been studied as an immune system in prokaryotes for the survival of bacteriophages. The CRISPR system in prokaryotes records the invasion of bacteriophages or other genetic materials in CRISPR loci. Accordingly, CRISPR loci can reveal a history of infection records of bacteriophages and other genetic materials. Therefore, identification of the CRISPR array may help trace the events that bacteria have undergone. In this study, we characterized and identified the spacers of the CRISPR loci in Escherichia coli isolates obtained from the feces of animals and humans. Most CRISPR spacers were found to stem from phages. Although we did not find any patterns in CRISPR spacers according to sources, our results showed that phage-derived spacers mainly originated from the families , , , and and the order , whereas plasmid-derived CRISPR spacers were mainly from the family. In addition, it is worth noting that the isolates from each animal and human source harbored source-specific spacers. Considering that some of these taxa are likely found in the gut of mammalian animals, CRISPR spacers identified in these E. coli isolates were likely derived from the bacteriophageome and microbiome in closed gut environments. Although the bacteriophageome database limits the characterization of CRISPR arrays, the present study showed that some spacers were specifically found in both animal and human sources. Thus, this finding may suggest the possible use of E. coli CRISPR spacers as a microbial source tracking tool. We characterized spacers of CRISPR locus 2.1 in E. coli isolates obtained from the feces of various sources. Phage-derived CRISPR spacers are mainly acquired from the order and plasmid-derived CRISPR spacers are mostly from the family. This is thought to reflect the microbiome and phageome of the gut environment of the sources. Hence, spacers may help track the encounter of bacterial cells with bacterial cells, viruses, or other genetic materials. Interestingly, source-specific spacers are also observed. The identification of source-specific spacers is thought to help develop the methodology of microbial source tracking and understanding the interactions between viruses and bacteria. However, very few spacers have been uncovered to track where they originate. The accumulation of genome sequences can help identify the hosts of spacers and can be applied for microbial source tracking.
成簇规律间隔短回文重复序列（CRISPR）作为原核生物中的一种免疫系统，已被用于研究噬菌体的生存情况。原核生物中的CRISPR系统会在CRISPR基因座中记录噬菌体或其他遗传物质的入侵情况。因此，CRISPR基因座可以揭示噬菌体和其他遗传物质的感染记录历史。所以，鉴定CRISPR阵列可能有助于追溯细菌所经历的事件。在本研究中，我们对从动物和人类粪便中分离出的大肠杆菌中的CRISPR基因座间隔序列进行了特征分析和鉴定。发现大多数CRISPR间隔序列来源于噬菌体。虽然我们未根据来源在CRISPR间隔序列中发现任何模式，但我们的结果表明，噬菌体来源的间隔序列主要源自 、 、 、 科以及 目，而质粒来源的CRISPR间隔序列主要来自 科。此外，值得注意的是，来自每种动物和人类来源的分离株都含有来源特异性间隔序列。考虑到这些分类群中的一些可能存在于哺乳动物的肠道中，在这些大肠杆菌分离株中鉴定出的CRISPR间隔序列可能源自封闭肠道环境中的噬菌体组和微生物组。尽管噬菌体组数据库限制了对CRISPR阵列的特征分析，但本研究表明，一些间隔序列在动物和人类来源中均有特异性发现。因此，这一发现可能表明大肠杆菌CRISPR间隔序列有可能用作微生物来源追踪工具。我们对从各种来源粪便中分离出的大肠杆菌中的CRISPR基因座2.1的间隔序列进行了特征分析。噬菌体来源的CRISPR间隔序列主要从 目获得，质粒来源的CRISPR间隔序列大多来自 科。这被认为反映了来源肠道环境中的微生物组和噬菌体组。因此，间隔序列可能有助于追踪细菌细胞与细菌细胞、病毒或其他遗传物质的相遇情况。有趣的是，也观察到了来源特异性间隔序列。来源特异性间隔序列的鉴定被认为有助于开发微生物来源追踪方法，并有助于理解病毒与细菌之间的相互作用。然而，很少有间隔序列被发现可追踪其起源。基因组序列的积累有助于鉴定间隔序列的宿主，并可应用于微生物来源追踪。
