Comparative genomic analysis of Fusobacterium nucleatum reveals high intra-species diversity and cgmlst marker construction.

IF 4.3 3区医学 Q1 GASTROENTEROLOGY & HEPATOLOGY

Gut Pathogens Pub Date : 2023-09-14 DOI:10.1186/s13099-023-00570-z

Qianhui Zhu, Arslan Dovletgeldiyev, Chen Shen, Kexin Li, Songnian Hu, Zilong He

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Abstract

Background: Fusobacterium nucleatum is a one of the most important anaerobic opportunistic pathogens in the oral and intestinal tracts of human and animals. It can cause various diseases such as infections, Lemierre's syndrome, oral cancer and colorectal cancer. The comparative genomic studies on the population genome level, have not been reported.

Results: We analyzed all publicly available Fusobacterium nucleatums' genomic data for a comparative genomic study, focusing on the pan-genomic features, virulence genes, plasmid genomes and developed cgmlst molecular markers. We found the pan-genome shows a clear open tendency and most of plasmids in Fusobacterium nucleatum are mainly transmitted intraspecifically.

Conclusions: Our comparative analysis of Fusobacterium nucleatum systematically revealed the open pan-genomic features and phylogenetic tree based on cgmlst molecular markers. What's more, we also identified common plasmid typing among genomes. We hope that our study will provide a theoretical basis for subsequent functional studies.

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比较基因组分析表明，核梭杆菌具有较高的种内多样性和cgmlst标记结构。

背景:核梭杆菌是人类和动物口腔和肠道中最重要的厌氧条件致病菌之一。它可以引起各种疾病，如感染、勒米尔综合征、口腔癌和结直肠癌。在种群基因组水平上的比较基因组研究尚未见报道。结果:我们分析了所有公开的核梭杆菌基因组数据，进行了比较基因组研究，重点研究了泛基因组特征、毒力基因、质粒基因组和开发的cgmlst分子标记。结果表明，核梭杆菌的泛基因组呈现明显的开放倾向，质粒主要在种内传播。结论:我们的比较分析系统地揭示了基于cgmlst分子标记的核梭杆菌开放的泛基因组特征和系统发育树。此外，我们还发现了基因组中常见的质粒分型。希望本研究能为后续的功能研究提供理论基础。

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来源期刊

Gut Pathogens GASTROENTEROLOGY & HEPATOLOGY-MICROBIOLOGY

CiteScore

7.70

自引率

2.40%

发文量

期刊介绍： Gut Pathogens is a fast publishing, inclusive and prominent international journal which recognizes the need for a publishing platform uniquely tailored to reflect the full breadth of research in the biology and medicine of pathogens, commensals and functional microbiota of the gut. The journal publishes basic, clinical and cutting-edge research on all aspects of the above mentioned organisms including probiotic bacteria and yeasts and their products. The scope also covers the related ecology, molecular genetics, physiology and epidemiology of these microbes. The journal actively invites timely reports on the novel aspects of genomics, metagenomics, microbiota profiling and systems biology. Gut Pathogens will also consider, at the discretion of the editors, descriptive studies identifying a new genome sequence of a gut microbe or a series of related microbes (such as those obtained from new hosts, niches, settings, outbreaks and epidemics) and those obtained from single or multiple hosts at one or different time points (chronological evolution).