环境微生物宏基因组学研究中的生物信息学方法

Bioinformatics tools and applications in the study of environmental microbial metagenomics

摘要:

高通量测序技术的发展促进了组学技术在环境微生物研究中的广泛应用，而宏基因组学是目前最为关键和成熟的组学方法。生物信息学在微生物宏基因组学研究中具有至关重要的作用。它贯穿于宏基因组学的数据收集和存储、数据处理和分析等各个阶段，既是宏基因组学推广的最大瓶颈，也是目前宏基因组学研究发展的关键所在。本文主要介绍和归纳了目前在高通量宏基因组测序中常用的生物信息学分析平台及其重要的信息分析工具。未来几年之内，测序成本的下降和测序深度的增加将进一步增大宏基因组学研究在数据存储、数据处理和数据挖掘层面的难度，因此相应生物信息学技术与方法的研究和发展也势在必行。近期内我们应该首先加强基础性分析和存储平台的建设以方便普通环境微生物研究者使用，同时针对目前生物信息分析的瓶颈步骤和关键任务重点突破，逐步发展。

Abstract:

The development of high-throughput sequencing technology promoted the wide applications of omics in the study of environmental microbiology. Among all omics technologies, metagenomics is the most critical and widely used method at present, while bioinformatics plays a very important role in its applications. The bioinformatic technologies were involved in metagenomics data collection, storage, preprocess and analysis. Therefore, it is not only the key of metagenomic development, but also the bottleneck for its implementation. This paper introduces the commonly used bioinformatic pipelines in both shotgun metagenome and amplicon of high-throughput sequencing. In next few years, the decline in cost and the increase in depth of high-throughput sequencing will dramatically elevate the difficulty on the analysis of metagenomic data. It is imperative to pay more and more attentions to develop the bioinformatics tools and analysis pipelines. Nowadays, we should strengthen the construction of fundamental analysis and storage platform to facilitate the data mining for ordinary microbial researchers. Meanwhile, we should develop more bioinformatic algorithms and tools to overcome the current bottleneck in the analysis of metagenomics.