Qian Chenggong, Ma Jiawen, Liang Jiale, Zhang Lei, Liang Xinle
School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.
Front Microbiol. 2022 Aug 2;13:951030. doi: 10.3389/fmicb.2022.951030. eCollection 2022.
is the predominant microbe in vinegar production, particularly in those natural fermentations that are achieved by complex microbial communities. Co-evolution of prophages with , including integration, release, and dissemination, heavily affects the genome stability and production performance of industrial strains. However, little has been discussed yet about prophages in . Here, prophage prediction analysis using 148 available genomes from 34 species was carried out. In addition, the type II toxin-antitoxin systems (TAs) and CRISPR-Cas systems encoded by prophages or the chromosome were analyzed. Totally, 12,000 prophage fragments were found, of which 350 putatively active prophages were identified in 86.5% of the selected genomes. Most of the active prophages (83.4%) belonged to the order dominated by the families and prophages (71.4%). Notably, strains survived in complex environments that frequently carried multiple prophages compared with that in restricted habits. prophages showed high genome diversity and horizontal gene transfer across different bacterial species by genomic feature characterization, average nucleotide identity (ANI), and gene structure visualization analyses. About 31.14% of prophages carry type II TAS, suggesting its important role in addiction, bacterial defense, and growth-associated bioprocesses to prophages and hosts. Intriguingly, the genes coding for Cse1, Cse2, Cse3, Cse4, and Cas5e involved in type I-E and Csy4 involved in type I-F CRISPR arrays were firstly found in two prophages. Type II-C CRISPR-Cas system existed only in , while the other species harbored the intact or eroded type I CRISPR-Cas systems. Totally, the results of this study provide fundamental clues for future studies on the role of prophages in the cell physiology and environmental behavior of .
是醋生产中的主要微生物，特别是在那些由复杂微生物群落实现的自然发酵过程中。原噬菌体与的共同进化，包括整合、释放和传播，严重影响工业菌株的基因组稳定性和生产性能。然而，关于中的原噬菌体，目前讨论较少。在此，利用来自34个物种的148个可用基因组进行了原噬菌体预测分析。此外，还分析了由原噬菌体或染色体编码的II型毒素-抗毒素系统（TAs）和CRISPR-Cas系统。总共发现了12000个原噬菌体片段，其中在86.5%的选定基因组中鉴定出350个推定活跃的原噬菌体。大多数活跃原噬菌体（83.4%）属于以和原噬菌体家族（71.4%）为主的目。值得注意的是，与在受限生境中的菌株相比，在复杂环境中存活的菌株经常携带多个原噬菌体。通过基因组特征表征、平均核苷酸同一性（ANI）和基因结构可视化分析，原噬菌体在不同细菌物种间表现出高度的基因组多样性和水平基因转移。约31.14%的原噬菌体携带II型TAS，表明其在原噬菌体和宿主的成瘾、细菌防御及与生长相关的生物过程中起重要作用。有趣的是，在两个原噬菌体中首次发现了参与I-E型的Cse1、Cse2、Cse3、Cse4和Cas5e以及参与I-F型CRISPR阵列的Csy4的编码基因。II-C型CRISPR-Cas系统仅存在于中，而其他33个物种含有完整或受损的I型CRISPR-Cas系统。总的来说，本研究结果为未来研究原噬菌体在细胞生理学和环境行为中的作用提供了基本线索。
