Vieites José M, Guazzaroni María-Eugenia, Beloqui Ana, Golyshin Peter N, Ferrer Manuel
CSIC, Institute of Catalysis, Madrid, Spain.
FEMS Microbiol Rev. 2009 Jan;33(1):236-55. doi: 10.1111/j.1574-6976.2008.00152.x. Epub 2008 Nov 24.
The world of microorganisms comprises a vast diversity of live organisms, each with its individual set of genes, cellular components and metabolic reactions that interact within the cell and communicate with the environment in many different ways. There is a strong imperative to gain a broader view of the wired and interconnected cellular and environmental processes as a whole via the systems microbiology approach in order to understand and predict ecosystem functioning. On the other hand, currently we experience a rise of metagenomics as an emerging tool to study communities of uncultured microorganisms. In this review, we conducted a survey of important methodologies in metagenomics and describe systems microbiology-like approaches for gaining a mechanistic understanding of complex microbial systems to interrogate compositional, evolutionary and metabolic properties. The review also discusses how metagenomics can be used as a holistic indicator for ecosystem response in terms of matter, nutrient and energy sources and functional networking.
微生物世界包含各种各样的活生物体，每一种都有其独特的基因、细胞成分和代谢反应，这些在细胞内相互作用，并以多种不同方式与环境进行交流。迫切需要通过系统微生物学方法，从整体上更全面地了解相互关联的细胞和环境过程，以便理解和预测生态系统功能。另一方面，目前宏基因组学作为一种研究未培养微生物群落的新兴工具正在兴起。在本综述中，我们对宏基因组学中的重要方法进行了调查，并描述了类似系统微生物学的方法，以深入了解复杂的微生物系统，从而探究其组成、进化和代谢特性。本综述还讨论了宏基因组学如何能够用作生态系统在物质、营养和能量来源以及功能网络方面响应的整体指标。
