环境微生物的宏基因组学研究新进展

doi:10.3724/SP.J.1003.2013.08050

摘要/Abstract

摘要：

宏基因组学以环境中微生物的基因组的总和为研究对象, 从而规避了传统方法中绝大部分微生物不能培养的缺陷, 因此近年来在环境微生物学研究中得到了广泛应用。本文重点介绍了宏基因组学技术中关键的两类技术: 即以罗氏454及Illumina为代表的高通量测序技术和以基因芯片(GeoChip)为代表的基因芯片技术在微生物研究中的应用。测序技术可以发现新物种和新基因, 但由于测序深度有限, 定量性差, 不易发现低丰度物种, 且易受污染物干扰。芯片技术很好地克服了这些局限, 但不易于发现新基因。本文介绍了这些技术近年来在气候变化、水处理工程系统、极端环境、人体肠道、石油污染修复、生物冶金等方面取得的部分代表性成果。在此基础上, 对宏基因组技术在环境微生物研究方面的未来发展方向提出了预判和展望。我们认为由于两种技术各自的优缺点, 今后将两类技术结合起来的综合研究会越来越多。另外, 由于大量数据的处理方法已成为制约宏基因组学发展的瓶颈, 相应的生物信息学技术开发将是未来科研的热点和难点。

关键词: 宏基因组学, 生物信息学, 高通量测序, 基因芯片

Abstract

Metagenomics is the study of microbial meta-genomes from environmental samples, which is independent on the ability to cultivate microbes in the laboratory. It provides a new way of examining the microbial world and has been widely used in microbiological research for the past decade. Sequencing-based metagenomic technology, represented by 454 and Illumina sequencing platforms, and microarray-based technology, often using GeoChip, are two of the most commonly used technologies in metagenomics. Sequencing-based technologies are capable of detecting new microbes and genes, but are limited with regard to sequence depth and quantification, and present problems of contamination when used on complex microbial communities. Microarray-based technologies are complementary to sequencing-based technologies in regard to advantages and disadvantages. They have been widely used, for example, in studies of climate change, energy, engineering, metallurgy, extreme environments and human health. However, their use in examining the extremely complex and diverse microbial world merits further technical development, with a focus on integrating both technologies and the development of appropriate bioinformatics tools.

Key words: metagenomics, bioinformatics, high-throughput sequencing, GeoChip

孙欣, 高莹, 杨云锋 (2013) 环境微生物的宏基因组学研究新进展. 生物多样性, 21, 393-400. DOI: 10.3724/SP.J.1003.2013.08050.

Xin Sun,Ying Gao,Yunfeng Yang (2013) Recent advancement in microbial environmental research using metagenomics tools. Biodiversity Science, 21, 393-400. DOI: 10.3724/SP.J.1003.2013.08050.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2013.08050

https://www.biodiversity-science.net/CN/Y2013/V21/I4/393

图/表 1

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方法 Technologies	高通量测序Sequencing	基因芯片Microarray
准确性 Accuracy	高 High	高 High
全面性 Coverage	高 High	高 High
信息深度 Depth	高 High	高 High
定量性 Quantification	低 Low	高 High
发现新物种 Detecting new species/genes	有 Yes	无 No
受污染物干扰 Interference by contaminants	高 High	低 Low
受群落主要物种干扰 Interference by abundant species	高 High	低 Low

方法 Technologies	高通量测序Sequencing	基因芯片Microarray
准确性 Accuracy	高 High	高 High
全面性 Coverage	高 High	高 High
信息深度 Depth	高 High	高 High
定量性 Quantification	低 Low	高 High
发现新物种 Detecting new species/genes	有 Yes	无 No
受污染物干扰 Interference by contaminants	高 High	低 Low
受群落主要物种干扰 Interference by abundant species	高 High	低 Low

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