16S rRNA基因在微生物生态学中的应用  

The applications of the 16S rRNA gene in microbial ecology: current situation and problems

作　　者：刘驰[1,2,3] 李家宝[1,2] 芮俊鹏 安家兴[1,2] 李香真[1,2] 

机构地区：[1]中国科学院环境与应用微生物重点实验室,成都610041 [2]环境微生物四川省重点实验室,中国科学院成都生物研究所,成都610041 [3]中国科学院大学,北京100049

出　　处：《生态学报》2015年第9期2769-2788,共20页Acta Ecologica Sinica

基　　金：国家重点基础研究发展规划资助项目(2013CB733502);国家自然科学基金资助项目(41371268,31300447)

摘　　要：16S rRNA(Small subunit ribosomal RNA)基因是对原核微生物进行系统进化分类研究时最常用的分子标志物(Biomarker),广泛应用于微生物生态学研究中。近些年来随着高通量测序技术及数据分析方法等的不断进步,大量基于16S rRNA基因的研究使得微生物生态学得到了快速发展,然而使用16S rRNA基因作为分子标志物时也存在诸多问题,比如水平基因转移、多拷贝的异质性、基因扩增效率的差异、数据分析方法的选择等,这些问题影响了微生物群落组成和多样性分析时的准确性。对当前使用16S rRNA基因分析微生物群落组成和多样性的进展情况做一总结,重点讨论当前存在的主要问题以及各种分析方法的发展,尤其是与高通量测序技术有关的实验和数据处理问题。The 16 S rRNA（ small subunit ribosomal RNA） gene is a universal marker for phylogenetic reconstructions to approximate the tree of life owing to its presence in all prokaryotes and its high conservation. Sequencing of 16 S rRNA genes amplified directly from environmental samples is commonly used to study microbial community composition and diversity.Great advances in pyrosequencing technology and bioinformatics in recent years enable us to obtain sequence data from large-scale environmental samples efficiently and cost-effectively. However,some critical problems need to be addressed when the 16 S rRNA gene is used for microbial diversity studies,such as horizontal gene transfer（ HGT）,intragenomic heterogeneity,PCR amplification efficiency,and sequencing data analysis. In this review,we summarize the state-of-theart applications of 16 S rRNA gene as a biomarker for microbial ecology studies,and introduce current pyrosequencing techniques and bioinformatics for large-scale data analysis. This review focuses on four aspects.（ i） We introduce the structure and properties of the 16 S rRNA gene,e. g. the primary and secondary structure,HGT and heterogeneities of 16 S rRNA genes. Based on current available microbial genomes,multi-copy and intragenomic heterogeneities of 16 S rRNA genes are recognized. These phenomena may seriously bias the estimations of microbial diversity in environmental samples.Some online tools and databases used for analysis of the 16 S rRNA gene sequencing data are also introduced. These toolsare used to predict horizontal gene transfer,secondary structure,and to align and classify 16 S rRNA gene sequences.（ ii）We introduce some 16 S rRNA-based techniques commonly used in microbial ecology studies,such as fingerprinting profiling,hybridization, microarray, and high throughput pyrosequencing methods. We compare the advantages and limitations of various methods and recommend how to use them properly based on a specific target. Different methods have different resolutions and detecti

关 键 词：16S RRNA基因 微生物群落 多样性 高通量测序 生物信息数据处理 

分 类 号：Q938[生物学—微生物学]