Analytical Approaches and Functional Insights for Microbiome Studies

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

Abstract

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

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.

Figures/Tables 4

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

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

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

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

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