快速基于基因组的Enterobacterales物种的划分
Julie E Hernández-Salmerón1, Tanya Irani1, Gabriel Moreno-Hagelsieb1
1Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada.
PloS one
|September 14, 2023
概括
像Mash和Dashing这样的快速基因组相似性估计,对于细菌物种划分的平均核酸标识 (ANI) 的表现也很好. 这些基于素描的方法在各种环境中提供了高效准确的细菌识别和聚类.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 微生物分类学 微生物分类学
背景情况:
- 平均核酸标识 (ANI) 是细菌物种划分的标准.
- 与基于草图的相似性估计相比,ANI计算需要大量的时间.
- 基于草图的方法相对于ANI的准确性需要进行彻底的评估.
研究的目的:
- 为了比较两个素描程序,Mash和Dashing的准确性,与细菌物种划分的ANI进行比较.
- 在细菌分类学中评估快速基因组相似性估计的实用性.
- 评估这些方法在各种细菌种群中的性能.
主要方法:
- 基于草图的Mash和Dashing与ANI的相似性估计的比较.
- 使用接收器操作特征 (ROC) 分析与曲线下的面积 (AUC) 来评估物种歧视.
- 对Enterobacterales基因组进行测试的方法,包括亚抽样和专注的属性分析.
主要成果:
- 马什和Dashing显示了高准确度 (AUC ≈0.99),与物种划界的ANI可比.
- 亚样本将AUC降低到0.92,仍然表明高度准确的歧视.
- 大多数属实现AUC>0.90,而Shigella和Citrobacter显示较低的值 (分别为0.68和0.80).
- 马什有效地将大肠杆菌和西格拉菌复合物分解为25个类组.
结论:
- 快速的基因组相似性估计与细菌物种划界的ANI一样有效.
- 基于素描的方法提供可靠的细菌识别和聚类.
- 这些发现增加了对使用高效的细菌分类学方法和污染检测等应用程序的信心.
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