基于高分辨率质谱的微生物宏代谢组解析方法研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2026-0429

生物技术通报 ›› 2026, Vol. 42 ›› Issue (5): 5-15.doi: 10.13560/j.cnki.biotech.bull.1985.2026-0429

基于高分辨率质谱的微生物宏代谢组解析方法研究进展

杨兴盛¹^,²(), 伍绍龙³(), 冯凯¹^,², 王尚¹^,², 彭玺¹^,², 赵博¹^,², 刘明倩¹^,², 顾松松¹^,², 何晴¹, 李春格¹, 胡秋龙⁴, 邓晔¹^,²()

^1.中国科学院生态环境研究中心，北京 100085
^2.中国科学院大学，北京 100049
^3.中国烟草总公司湖南省公司，长沙 410004
^4.湖南农业大学，长沙 410128

收稿日期:2026-04-15 出版日期:2026-05-26 发布日期:2026-06-10
通讯作者: 伍绍龙，男，博士，高级农艺师，研究方向：烟草智慧农业；E-mail: slwuhnyc@126.com
邓晔，男，博士，研究员，研究方向：环境微生物组学；E-mail: yedeng@rcees.ac.cn
作者简介:杨兴盛，男，博士研究生，研究方向：微生物组和宏代谢组；E-mail: yangxingsheng18@mails.ucas.ac.cn
基金资助:
国家科技重大专项“深地复杂地质环境与微生物适应条件”(2024ZD1000601);中国烟草总公司重点研发项目(110202402009)

Progress in High-resolution Mass Spectrometry‑based Approaches for Microbial Meta‑metabolomics

YANG Xing-sheng¹^,²(), Wu Shao-long³(), FENG Kai¹^,², WANG Shang¹^,², PENG Xi¹^,², ZHAO Bo¹^,², LIU Ming-qian¹^,², GU Song-song¹^,², HE Qing¹, LI Chun-ge¹, Hu Qiu-long⁴, DENG Ye¹^,²()

^1.Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085
^2.University of Chinese Academy of Sciences, Beijing 100049
^3.Tobacco Company of Hunan Province, Changsha 410004
^4.Hunan Agricultural University, Changsha 410128

Received:2026-04-15 Published:2026-05-26 Online:2026-06-10

摘要/Abstract

摘要：

深入揭示微生物代谢的调控机制与生态功能，对理解有机物地球化学循环、预测碳-气候反馈以及工程应用中调控碳流具有重要意义。微生物宏代谢组学将有机分子视为“分子群落”，从群落水平整体考察代谢产物的组成与动态。高分辨率质谱技术为大规模解析有机代谢物分子信息提供了有力手段，得到的分子指纹可以借鉴生态学分析方法进行深入挖掘。然而，该领域仍面临代谢物-功能关联障碍及过程归因困难。本综述系统梳理了宏代谢组学的最新方法进展，包括生态学机制的扩展应用、分子生态网络构建及多维度分子特征分析，并剖析了当前技术局限性。最后，从发展多组学时空耦合分析、关键代谢角色识别及生态理论拓展等方面对未来研究方向进行了展望，以推动该领域成为解析生态系统功能与碳调控研究的前沿支撑。

关键词: 宏代谢组, 生态过程, 分子生态网络, 分子特征

Abstract:

Elucidating the regulatory mechanisms and ecological functions of microbial metabolism is crucial for understanding the carbon biogeochemical cycling, predicting carbon-climate feedbacks, and modulating carbon flows in engineered applications. Microbial meta-metabolomics conceptualizes organic molecules as a “molecular community”, enabling a holistic investigation into the composition and dynamics of metabolites at the community level. High-resolution mass spectrometry has emerged as a powerful approach for large-scale profiling of organic metabolites, and the resulting molecular fingerprints can be deeply explored by leveraging ecological analytical frameworks. However, challenges remain in linking metabolites to microbial functions and attributing metabolic processes. This review systematically summarizes recent methodological advances in meta-metabolomics, including the extended application of ecological mechanisms, the construction of molecular ecological networks, and multi-dimensional molecular profiling, while also highlighting current technical limitations. Looking forward, integrating multi-omics spatiotemporal analyses, identifying key metabolic roles, and extending ecological frameworks will be critical for establishing this field as a frontier in understanding ecosystem functions and carbon regulation.

Key words: meta?metabolomics, ecological processes, molecular ecological network, molecular feature

杨兴盛, 伍绍龙, 冯凯, 王尚, 彭玺, 赵博, 刘明倩, 顾松松, 何晴, 李春格, 胡秋龙, 邓晔. 基于高分辨率质谱的微生物宏代谢组解析方法研究进展[J]. 生物技术通报, 2026, 42(5): 5-15.

YANG Xing-sheng, Wu Shao-long, FENG Kai, WANG Shang, PENG Xi, ZHAO Bo, LIU Ming-qian, GU Song-song, HE Qing, LI Chun-ge, Hu Qiu-long, DENG Ye. Progress in High-resolution Mass Spectrometry‑based Approaches for Microbial Meta‑metabolomics[J]. Biotechnology Bulletin, 2026, 42(5): 5-15.

图/表 4

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研究体系 Research system	实验设计 Experimental design	核心数据 Core data	数据分析方法 Data analysis methods	参考文献 References
冻土	冻土融化梯度；3个深度采样	12T FTICR 负离子采集；100-1 200 m/z；<1 ppm；分子14432；宏基因组1402MAGs	微生物和代谢物在群落和个体水平的生态构建过程；共现网络	［31］
土壤	生物圈2号热带雨林；模拟干旱环境；同位素标记	12T FTICR 负离子采集；100-1 000 m/z；<1 ppm；分子数未报道；宏基因组和转录组	代谢功能注释和关联	［50］
土壤	施肥处理	9.4T FTICR 负离子采集；150-800 m/z；分子 7682	转化网络；应用机器学习基于分子特性预测转化潜力	［35］
热融湖塘	青藏高原1 100 km多年冻土带沿线10个热熔湖塘；阳光和微生物降解实验	15T FTICR 负离子采集；100-800 m/z；<1 ppm；分子数未报道；扩增子测序	对分子组成和分子的特征分析	［24］
基于湖泊水体的微宇宙实验	中国和挪威的2座山，5个不同海拔	15T FTICR 负离子采集；150-1 200 m/z；<1 ppm；分子19538；扩增子测序	代谢物的生态构建过程；分子持久性和转化活性分析	［18］
滩涂沉积物	沿海岸线采样	15T FTICR 负离子采集；200-800 m/z；<1 ppm；分子20980；扩增子测序	微生物和有机分子组成在生态模式上的比较	［25］
厌氧发酵罐	7个城市，6个时间序列	15T FTICR 负离子采集；100-800 m/z；<1 ppm；分子28925；宏基因组413MAGs；扩增子测序2960OTUs	加权分子特性；转化识别；共现网络	［29］

研究体系 Research system	实验设计 Experimental design	核心数据 Core data	数据分析方法 Data analysis methods	参考文献 References
冻土	冻土融化梯度；3个深度采样	12T FTICR 负离子采集；100-1 200 m/z；<1 ppm；分子14432；宏基因组1402MAGs	微生物和代谢物在群落和个体水平的生态构建过程；共现网络	［31］
土壤	生物圈2号热带雨林；模拟干旱环境；同位素标记	12T FTICR 负离子采集；100-1 000 m/z；<1 ppm；分子数未报道；宏基因组和转录组	代谢功能注释和关联	［50］
土壤	施肥处理	9.4T FTICR 负离子采集；150-800 m/z；分子 7682	转化网络；应用机器学习基于分子特性预测转化潜力	［35］
热融湖塘	青藏高原1 100 km多年冻土带沿线10个热熔湖塘；阳光和微生物降解实验	15T FTICR 负离子采集；100-800 m/z；<1 ppm；分子数未报道；扩增子测序	对分子组成和分子的特征分析	［24］
基于湖泊水体的微宇宙实验	中国和挪威的2座山，5个不同海拔	15T FTICR 负离子采集；150-1 200 m/z；<1 ppm；分子19538；扩增子测序	代谢物的生态构建过程；分子持久性和转化活性分析	［18］
滩涂沉积物	沿海岸线采样	15T FTICR 负离子采集；200-800 m/z；<1 ppm；分子20980；扩增子测序	微生物和有机分子组成在生态模式上的比较	［25］
厌氧发酵罐	7个城市，6个时间序列	15T FTICR 负离子采集；100-800 m/z；<1 ppm；分子28925；宏基因组413MAGs；扩增子测序2960OTUs	加权分子特性；转化识别；共现网络	［29］

基于高分辨率质谱的微生物宏代谢组解析方法研究进展

Progress in High-resolution Mass Spectrometry‑based Approaches for Microbial Meta‑metabolomics

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