对测序平台的比较评估:太平洋生物科学,牛津纳米孔技术和Illumina用于基于16S rRNA的土壤微生物组概况
Vladimir Veselovsky1, Mikhail Romanov1, Polina Zoruk1
1Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
Frontiers in microbiology
|August 22, 2025
概括
像牛津纳米孔技术 (ONT) 和太平洋生物科学 (PacBio) 这样的长期测序技术准确地描述了土壤微生物组. 微生物群体分析有效地按土壤类型分组样本,不论测序平台或目标区域,V4区域除外.
科学领域:
- 微生物生态学
- 基因组学
- 生物信息学
背景情况:
- 对于了解生态系统功能和农业生产力至关重要.
- 包括太平洋生物科学 (PacBio) 和牛津纳米孔技术 (ONT) 在内的高吞吐量测序已经进行了先进的微生物社区分析.
- 长读数测序为细致的微生物多样性评估提供了增强的能力.
研究的目的:
- 使用Illumina,PacBio和ONT测序平台对土壤微生物群的细菌多样性进行比较评估.
- 评估不同16S rRNA基因区域 (全长,V4,V3-V4) 对微生物群体分析的影响.
- 确定长读数测序技术 (PacBio和ONT) 与短读数测序技术 (Illumina) 的可比性.
主要方法:
- 使用Illumina (V4,V3-V4),PacBio (全长,修剪V3-V4/V4) 和ONT (全长) 进行了16S rRNA基因测序.
- 用标准化生物信息管道分析了三种不同的土壤类型.
- 测序深度在各个平台上正常化 (10,00035,000读数) 以便进行比较.
主要成果:
- ONT和PacBio的细菌多样性评估结果相似,PacBio的细菌多样性检测结果略好.
- ONT测序结果与PacBio非常相匹配,表明测序错误对充分代表的类型的影响很小.
- 微生物群体分析在V4区域 (p=0.79) 以外,在不同平台和目标区域中一致地按土壤类型分组样本.
结论:
- 无论是PacBio还是ONT都是可靠的土壤微生物组概况和细菌多样性评估.
- 不管测序技术或目标区域,可以根据土壤类型识别微生物群落结构,V4区域是例外.
- 该研究提供了对土壤微生物组研究的测序平台性能的全面评估.
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