Biodiversity Science ›› 2013, Vol. 21 ›› Issue (4): 393-400.doi: 10.3724/SP.J.1003.2013.08050

Special Issue: Microbes Diversity

• Orginal Article • Previous Article     Next Article

Recent advancement in microbial environmental research using metagenomics tools

Xin Sun, Ying Gao, Yunfeng Yang*()   

  1. State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084
  • Received:2013-02-26 Accepted:2013-05-09 Online:2013-07-29
  • Yang Yunfeng

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

Table 1

Comparison of high throughput-sequencing and GeoChip technologies"

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
Detecting new species/genes
有 Yes 无 No
Interference by contaminants
高 High 低 Low
Interference by abundant species
高 High 低 Low
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