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Functional metagenomic profiling of nine biomes
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近1500万个基因组序列，被用在对来自从珊瑚礁和河流到矿井深处在内的9个不同类型的生态系统的45个微生物基因组（microbiomes）和42个病毒基因组（viromes）（后者为噬菌体所主导）的一项环境基因组比较研究中。虽然核心代谢特征在来自所有环境的微生物基因组中都有代表，但根据关于代谢功能的一个列表，研究人员在9个不同生态系统的每一个中都发现了微生物的一个特征指纹。这项分析还揭示了一组意外的病毒代谢功能，说明病毒可能充当供它们的微生物宿主之间共享基因的一个基因库。 Microbial activities shape the biogeochemistry of the planet1, 2 and macroorganism health3. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes. Nature 452, 629-632 (3 April 2008) | doi:10.1038/nature06810; Received 18 November 2007; Accepted 6 February 2008; Published online 12 March 2008 |
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