微生物组分析方法与功能挖掘

doi:10.13560/j.cnki.biotech.bull.1985.2024-0788

摘要/Abstract

摘要：

微生物是生命科学研究中不可或缺的重要资源，其研究对推动科学进步、促进人类健康和改善环境质量等具有重要意义。随着二、三代高通量测序技术的迅猛发展，我们对微生物世界的认知得到了极大提升，在面对大量的微生物组数据时，选择适当的分析方法以实现快速、准确的信息挖掘显得尤为关键。本文对近年来微生物组研究的进展进行了系统的回顾与分析，着重更新了扩增子、培养组和宏基因组等二代短读序宏基因组数据的分析工具，纳入了三代长读序宏基因数据的处理方案，并提出了标准化数据分析流程的必要性。此外，本文结合解析微生物组的实例案例，侧重介绍其在植物与根系微生物互作、微生物多样性等方面的应用实例，探讨了不同方法在微生物组构成、结构和功能分析中的优劣，展示了宏基因组数据挖掘在应用方面的潜力，以期拓宽宏基因组数据挖掘的研究思路。最后，本文指出了当前微生物组研究中的不足和面临的挑战，并展望了未来微生物组研究技术的标准化与流程化方面的发展趋势，以期加速微生物组的功能与应用的研究进程。

关键词: 微生物组, 宏基因组, 扩增子, 分析方法, 功能挖掘

Abstract:

Microbiomes are crucial resources in life science, playing vital roles in advancing scientific knowledge, promoting human health, and improving environmental quality. The rapid evolution of second- and third-generation metagenomic technologies has greatly enhanced our understanding of microbial world. With the proliferation of microbiome data, the need to select appropriate analytical methods for efficiently extracting information has become increasingly essential. Here, we provide a comprehensive review of recent progress in microbiome studies, focusing on updated analytical tools for short-read second-generation sequencing data, including amplicon, culture-based methods, and metagenomic data. In addition, we offer the processing strategies for long-read third-generation sequencing data. We highlight the necessity for standardized data analysis workflows and present case studies that demonstrate the application of these methods in exploring microbiome interactions, particularly in plant and root-associated microbial systems. We discuss the strengths and limitations of various methods in analyzing microbiome composition, structure, and functionality, highlighting the potential of metagenomic data mining for practical applications. Finally, we address current limitations and challenges in microbiome study, and we discuss future trends toward the standardization and streamlining of microbiome study methodologies to accelerate progress in understanding microbiome functions and applications.

Key words: microbiome, metagenome, amplicon, analytical methods, functional exploration

高云云, 杨海飞, 吕虎杰, 刘永鑫. 微生物组分析方法与功能挖掘[J]. 生物技术通报, 2024, 40(10): 98-107.

GAO Yun-yun, YANG Hai-fei, LYU Hu-jie, LIU Yong-xin. Analytical Approaches and Functional Insights for Microbiome Studies[J]. Biotechnology Bulletin, 2024, 40(10): 98-107.

图/表 4

图1 微生物组研究的发展与应用 A：微生物组研究的应用场景；B：重大的技术和方法发展推动微生物组的研究；C：微生物组研究热点的发展趋势

Fig. 1 Development and application of microbiome study A: Application scenarios of microbiome study. B: Significant technological and methodological developments driving microbiome study. C: Trends in key areas of microbiome study

图2 基于二代高通量测序技术的分析流程和应用方案

Fig. 2 Analysis workflow and applications based on second-generation high-throughput sequencing technology

图3 基于宏基因组分析探讨植物与根际微生物的互作对植物营养吸收影响的案例 A：提出科学假设；根据籼稻氮肥利用效率高于粳稻这一科学现象提出，水稻和根际微生物组如何互作影响氮肥的利用效率这一科学假设；B：开展实践方案；基于扩增子、宏基因组、培养组分析，发现籼粳稻根系微生物组差异分析、根系微生物组差异受NRT1.1B基因调控、水稻根系微生物培养和合成菌群改变水稻氮吸收实验的实践方案；C：获取理论验证；特定根系微生物会参与有机氮矿化的过程促进水稻的氮元素吸收，且该现象与硝酸盐转运蛋白基因NRT1.1B在籼粳稻之间的自然变异相关联

Fig. 3 Case study on the effects of plants-rhizosphere microorganism interaction on plant nutrient uptake based on metagenomic analysis A: Develop scientific hypotheses. Based on the observation that nitrogen use efficiency of indica rice is higher than that of japonica rice, the hypothesis that rice and the rhizosphere microbiome interact to influence nitrogen use efficiency is proposed. B: Implement practical programs. Utilizing amplification, metagenomic analysis, and culture group analysis, the differences in root microbiomes between indica and japonica rice are examined. Additionally, the role of the NRT1.1B gene in regulating these differences is investigated, and experiments are conducted on the cultivation of rice root microbiomes and synthetic communities to assess changes in nitrogen absorption. C: Theoretical validation. Specific root microbiomes participate in the process of organic nitrogen mineralization, thereby enhancing nitrogen uptake in rice. This phenomenon is linked to the natural variation of the nitrate transporter gene NRT1.1B between indica and japonica rice

图4 基于三代纳米孔技术的分析流程和应用方案

Fig. 4 Analysis workflow and applications based on third-generation nanopore technology

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