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少量的错组装可能对基于泛基因组的元基因组分析产生不成比例的影响
Stephanie N Majernik1, Larry Beaver1, Patrick H Bradley1,2,3
1Dept. of Microbiology, The Ohio State University, Columbus, OH 43210 USA.
bioRxiv : the preprint server for biology
|October 17, 2024
概括
来自元基因组的微生物基因分析容易受到污染,导致错误的关联. 一种名为PanSweep的新方法识别和去除污染物,揭示了肠道微生物运动和肝硬化之间的联系.
科学领域:
- 微生物组研究的研究.
- 转基因组学是指转基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 微生物基因影响宿主表型,使其准确的识别至关重要.
- 超基因组工具估计微生物基因拷贝数量,使用来自物种基因组的泛基因组.
- 来自混合社区的元基因组组装基因组 (MAG) 可以污染泛基因组,影响下游分析.
研究的目的:
- 调查污染对基于泛基因组的元基因组分析的影响.
- 开发和验证一种用于识别和清除污染物的方法.
- 重新评估肠道微生物基因与污染物清除后肝硬化之间的关联.
主要方法:
- 在肝硬化患者的病例控制肠道微生物组研究的重新分析.
- 在开始性Clostridia中识别差异性流行基因.
- 序列相似性搜索和基因与物种的相关性与旗污染物.
- 开发PanSweep分析和可视化管道的开发.
主要成果:
- 在初步分析中,38%的差异性流行基因被确定为污染物.
- 污染物来源于与之无关的属,例如Veillonella和Haemophilus.
- 一种基因与物种的相关性方法准确地确定了大多数污染物.
- 在去除污染物后,Lachnospira eligens中的鞭毛运动基因集群与肝硬化有关.
结论:
- 在元基因组组合中,即使是低水平的污染也可以显著偏差基因水平分析.
- 泛扫管道有效地识别和减轻泛基因组污染.
- 这种方法揭示了肠道微生物鞭毛运动性和肝硬化之间的新兴联系.
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