摘要：

微生物组是指一个特定环境或生态系统中全部微生物及其遗传信息的集合, 其蕴藏着极为丰富的微生物资源。全面系统地解析微生物组的结构和功能, 将为解决人类面临的能源、生态环境、工农业生产和人体健康等重大问题带来新思路。然而, 微生物组学研究在很大程度上取决于其技术与方法的发展。在高通量测序技术出现以前, 微生物研究主要基于分离培养和指纹图谱等技术, 然而, 由于这些技术存在的缺陷, 人们对于微生物的认识十分有限。自21世纪初以来, 尽管高通量测序和质谱技术的革命性突破极大地促进了人们对于微生物的认识, 微生物组学技术在微生物组研究中的应用仍面临着诸多挑战。此外, 目前微生物组的结构和多样性等描述性研究已臻成熟, 微生物组学研究正处于从数量到质量、从结构到功能的关键转变时期。因此, 该文首先介绍了微生物组学的基本概念及其发展简史, 其次简述了微生物组学研究的相关技术和方法及其发展历程, 并进一步阐述了微生物组学的技术和方法在生态学研究中的应用及存在的主要问题, 最后从技术、理论和应用层面阐述了未来微生物组学技术和方法发展的前沿方向, 并提出了今后微生物组学研究的优先发展领域。

微生物功能

Abstract:

Microbiome is the combination of all microorganisms and their genetic information in a specific environment or ecosystem, which contains abundant microbial resources. A comprehensive and systematic analysis of the structure and function of microbiome will provide new ideas in solving the core issues in the fields of energy, ecological environment, industrial and agricultural production and human health. However, the study of microbiome largely depends on the development of relevant technologies and methods. Before to the advent of high-throughput sequencing technology, microbial research was mainly based on techniques such as isolation, pure-culture and fingerprint. However, due to the technical restrictions, scientists could only get limited knowledge of microorganisms. Since the beginning of 21st century, the revolutionary advances in the technology of high-throughput sequencing and mass spectrometry have greatly improved our understanding on the structure and ecological functions of environmental microbiome. However, the application of microbiomics technology in microbial research still faces many challenges. In addition, the descriptive studies focusing on the structure and diversity of microbiome have already matured, and the study of microbiomics is facing a critical transition period from quantity to quality and from structure to function. Hence, this paper will firstly introduce the basic concepts of microbiomics and a brief development history. Secondly, this paper introduces the related technologies and methods of microbiomics with their development process, and further expounds the applications and main problems of microbiomics technologies and methods in ecological study. Finally, this paper expounds the frontier direction of the development of microbiomics technology and methods from the technical, theoretical and application levels, and proposes the priority development areas of microbiome research in the future.

Key words: microbiomics, high-throughput sequencing, mass spectrometry, microbial functions 图1 历年来发表的微生物组学相关文章数量趋势图。A, 包含关键词“微生物组”的文章数。B, 包含关键词“微生物”且分别包含“宏代谢组学”“宏蛋白质组学”“宏基因组学”“宏转录组学”的文章数量。数据来源于Web of Science核心文集(时间: 1900-2019年)。 Fig. 1 Tendency of the published articles in microbiome over years. A, Number of articles with the keyword “microbiome”. B, Number of articles with the keyword “(‘microorganism*’ or ‘microbe*’ or ‘bacter*’ or ‘archae*’ or ‘fung*’)” and “metagenomics”, “metatranscriptomics”, “metaproteomics” and “metabolomics”, respectively. Data were collected from Web of Science Core Collection (Time: 1900-2019).

图1 历年来发表的微生物组学相关文章数量趋势图。A, 包含关键词“微生物组”的文章数。B, 包含关键词“微生物”且分别包含“宏代谢组学”“宏蛋白质组学”“宏基因组学”“宏转录组学”的文章数量。数据来源于Web of Science核心文集(时间: 1900-2019年)。

Fig. 1 Tendency of the published articles in microbiome over years. A, Number of articles with the keyword “microbiome”. B, Number of articles with the keyword “(‘microorganism*’ or ‘microbe*’ or ‘bacter*’ or ‘archae*’ or ‘fung*’)” and “metagenomics”, “metatranscriptomics”, “metaproteomics” and “metabolomics”, respectively. Data were collected from Web of Science Core Collection (Time: 1900-2019).

主导部门 Department	启动时间 Starting year	计划名称 Project name
美国国立卫生研究院 US National institutes of Health	2007	人体微生物组计划 The Human Microbiome Project
美国阿贡国家实验室 Argonne National Laboratory	2010	地球微生物组计划 Earth Microbiome Project
巴西国家科学技术研究院 Instituto Nacional de Pesquisas Espaciais	2013	巴西微生物组计划 The Brazilian Microbiome Project
美国白宫科学和技术政策办公室与联邦机构、私营基金管理机构 Office of Science and Technology Policy, Federal Agency, Private Fund Management Agency	2016	国家微生物组计划 National Microbiome Initiative
南非和美国国际开发署 South Africa and United States Agency for International Development	2016	非洲土壤微生物组计划 African Soil Microbiology Project
中国科学院 Chinese Academy of Sciences	2017	中国微生物组计划 China Microbiome Initiative

表1 全球重大“微生物组计划”一览

Table 1 General survey of ‘Microbiome Project’ in the world

主导部门 Department	启动时间 Starting year	计划名称 Project name
美国国立卫生研究院 US National institutes of Health	2007	人体微生物组计划 The Human Microbiome Project
美国阿贡国家实验室 Argonne National Laboratory	2010	地球微生物组计划 Earth Microbiome Project
巴西国家科学技术研究院 Instituto Nacional de Pesquisas Espaciais	2013	巴西微生物组计划 The Brazilian Microbiome Project
美国白宫科学和技术政策办公室与联邦机构、私营基金管理机构 Office of Science and Technology Policy, Federal Agency, Private Fund Management Agency	2016	国家微生物组计划 National Microbiome Initiative
南非和美国国际开发署 South Africa and United States Agency for International Development	2016	非洲土壤微生物组计划 African Soil Microbiology Project
中国科学院 Chinese Academy of Sciences	2017	中国微生物组计划 China Microbiome Initiative

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