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从微生物群体中预测未经表征的基因产品的功能

Yancong Zhang^1,2,3,4, Amrisha Bhosle^5,6,7, Sena Bae^6,7,8

¹Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China. zhangyancong@caas.cn.

Nature biotechnology

|October 15, 2025

概括

研究人员开发了一种新方法,使用多组学数据来确定微生物蛋白质的功能. 这种方法成功地特征了超过443,000个蛋白质家族,大大扩大了我们对人类肠道微生物组的理解.

科学领域:

微生物学微生物学
生物信息学是一种生物信息学.
基因组学就是基因组学.

背景情况:

大多数微生物基因缺乏特征功能,这阻碍了我们对微生物社区角色的理解.
现有的蛋白质功能预测方法对于复杂的微生物群体的范围和可扩展性往往是有限的.

研究的目的:

开发和验证一种可扩展的方法来推断微生物蛋白质的假定功能,使用社区范围的多组学数据.
在人类肠道微生物群中显著增加特征蛋白家族的数量.

主要方法:

应用了一种新的方法,FUGAsseM,分析来自肠道元基因组和转录元基因组的多基因组数据.
集成序列相似性,基因组接近性和域间相互作用,以提高功能预测的准确性.
超过443,000个蛋白质家族的预测功能,包括那些与已知的蛋白质具有弱或无同质性的蛋白质.

主要成果:

成功预测了82.3%的分析蛋白家族的高置信函数 (>443,000总数).
确定了成千上万个以前未被描述的蛋白质家族的功能,包括那些缺乏同质性的蛋白质家族.
证明了FUGAsseM在各种微生物群落中的通用性,以及其与单个生物体方法相比的准确性.

结论:

FUGAsseM方法显著扩大了微生物蛋白的功能注释,特别是在缺乏特征的社区.
这项工作为探索微生物生态系统的功能格局提供了一个强大的工具,从人类肠道微生物组开始.

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