对16S rRNA基因序列的评估和基于基因组的分析,用于识别非致病性Yersinia

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Updated: May 31, 2025

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Angelina A Kislichkina¹, Angelika A Sizova¹, Yury P Skryabin²

¹Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia.

Frontiers in microbiology

|January 23, 2025

概括

由于高度相似性和基因内变异性,16S rRNA基因测序难以识别非致病性Yersinia. 基于基因组的分析,使用核心SNP和平均核酸标识 (ANI),为准确的Yersinia物种识别提供了卓越的区分能力.

科学领域:

微生物学微生物学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

16S rRNA基因测序是细菌识别的标准,但面临着局限性.
16S rRNA基因中的高序列相似性和基因内异质性可能会阻碍精确的物种歧视.
识别非致病性Yersinia物种对于公共卫生和研究至关重要.

研究的目的:

为了比较16S rRNA基因测序与基于基因组的分析用于识别非致病性Yersinia物种的区分能力.
为了评估核心单核酸多态 (SNP) 和平均核酸身份 (ANI) 对Yersinia分类学的实用性.
评估Yersinia基因组内的16S rRNA基因异质性的程度.

主要方法:

使用了来自NCBI的373个Yersinia菌株的完整和草稿基因组.
使用核心SNP和ANI进行基因组分析.
分析了16S rRNA基因序列,以查看菌株内部和跨菌株的同质性和变异性.
比较来自16S rRNA基因数据的分类学赋值与基于基因组的方法.

主要成果:

基于基因组的分析 (核心SNP和ANI) 揭示了与NCBI注释相比34个Yersinia基因组的分类学差异.
16S rRNA基因的基因内同质性在完整基因组中超过99.5%,超过50%的基因组表现出四种或更多的变异.
11%的基因组草案缺乏全长的16S rRNA基因,排除了基因内异质性评估.
在Y.intermedia和Y.rochesterensis的菌株中发现了相同的16SrRNA基因序列,这些菌株基于ANI和核心SNP而有所区别.
基于16S rRNA基因的家族遗传树并没有准确地反映Yersinia物种之间的基因组关系.

结论:

由于序列相似性和基因内异质性,16S rRNA基因测序不足以准确识别密切相关的非致病性Yersinia物种.
基于基因组的分析,特别是核心SNP和ANI,为Yersinia分类学提供了更高的分辨率和可靠性.
这项研究强调了需要基于基因组的方法来解决分类学模两可,并改善研究不足的Yersinia物种的表征.

关键词:

16S rRNA 是一个16S rRNA.一年多的时间.在WGS中,使用的是WGS.耶尔西尼亚尼亚是什么意思核心SNP的核心SNP是什么基因组基因组是基因组的组成部分.人类的基因组学.分类学分类学.

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