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整个元基因组测序:没有深度足以完全恢复微生物功能

Jia Liu, Modupe Oluseun Coker, Nosayaba Osazuwa-Peters

bioRxiv : the preprint server for biology

|November 24, 2025

概括

整个元基因组射击枪测序 (WMS) 的技术变异性可以掩盖微生物的功能. 优化测序深度和注释策略对于准确的微生物组功能推断和可重现的结果至关重要.

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:

整个元基因组射击枪测序 (WMS) 对微生物功能进行分析至关重要.
技术变化,包括批量效应,使大规模WMS数据分析复杂化.
需要对影响WMS功能推理的因素进行系统评估.

研究的目的:

评估技术因素对WMS数据中的功能推理的影响.
评估测序深度和注释策略对微生物功能恢复的影响.
开发一个框架来优化WMS研究设计.

主要方法:

分析了671名尼日利亚年轻人的口腔冲洗WMS数据.
使用米相/融合和HUMAnN 3/EC数量管道进行微生物功能的注释.
技术因素对功能恢复的影响的量化.

主要成果:

注释策略会影响功能覆盖范围的广度和具体性.
在浅的测序深度下,低发病率的功能会丢失,影响研究分辨率.
增加序列深度并不能比例地改善功能回忆;功能回忆的很大一部分仍然无法检测到.

结论:

结果为WMS研究设计和解释提供了实际指导方针.
协调测序深度,注释策略和批量控制对于强大的微生物功能检测至关重要.
可复制的微生物群洞察力取决于严格的方法规划.

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