未培养微生物研究:方法、机遇与挑战

Uncultivated microorganisms study: methods, opportunities and challenges

摘要:

自然界中绝大部分的微生物仍是未培养的，称之为未培养微生物或微生物“暗物质”。对其进行研究不仅有助于认识微生物多样性及其代谢特征，加深对环境中微生物参与的生态学过程的理解，还有利于重构生命之树，揭示微生物的进化历程，具有重要的科学意义。同时未培养微生物是发现新基因资源和新活性物质的巨大宝库。随着现代分子生物学研究方法和培养技术的成熟和完善，从环境中直接破译未培养微生物的遗传信息，并实现培养逐渐成为可能。本文主要介绍了基于宏基因组技术和单细胞基因组技术或两者结合运用，研究环境中未培养微生物的主要方法和挑战，总结分析了目前已经解析的未培养微生物的主要类群，并对未来研究的机遇进行了展望。

Abstract:

The majority of microbial species in the environment remains uncultivated, called uncultivated microorganisms or microbial "dark matter". Unraveling the mysteries of these microbial "dark matter" is especially important to understand the diversity of microbes and their metabolic characteristics. These data can provide insights into the microbes involved in ecological processes, and insights into the early diversification of microbial lineages and the evolution of Bacteria and Archaea. DNA genome sequences of microbial "dark matter" could be recovered from the environment samples by population binning of metagenomics and single-cell genomics, independently or combined synergistically. The metabolic potential could be predicted based on bioinformatics analysis. In this mini-review, we briefly introduce the methods and challenges in this area, summarize the main groups of microbial "dark matter" that has been explored, and indicate the future research opportunities.