Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark.
Nat Biotechnol. 2013 Jun;31(6):533-8. doi: 10.1038/nbt.2579. Epub 2013 May 26.
Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition-independent approach to recover high-quality microbial genomes from deeply sequenced metagenomes. Multiple metagenomes of the same community, which differ in relative population abundances, were used to assemble 31 bacterial genomes, including rare (<1% relative abundance) species, from an activated sludge bioreactor. Twelve genomes were assembled into complete or near-complete chromosomes. Four belong to the candidate bacterial phylum TM7 and represent the most complete genomes for this phylum to date (relative abundances, 0.06-1.58%). Reanalysis of published metagenomes reveals that differential coverage binning facilitates recovery of more complete and higher fidelity genome bins than other currently used methods, which are primarily based on sequence composition. This approach will be an important addition to the standard metagenome toolbox and greatly improve access to genomes of uncultured microorganisms.
参考基因组对于理解微生物在生态、进化、人类和动物健康中的多样作用至关重要，但大多数微生物仍未被培养。在这里，我们提出了一种不依赖序列组成的方法，可从深度测序的宏基因组中恢复高质量的微生物基因组。我们使用同一群落的多个宏基因组（相对丰度不同），组装了 31 个细菌基因组，包括来自活性污泥生物反应器的稀有（<1%相对丰度）物种。12 个基因组被组装成完整或近乎完整的染色体。其中 4 个属于候选细菌门 TM7，是迄今为止该门最完整的基因组（相对丰度为 0.06-1.58%）。对已发表的宏基因组的重新分析表明，差异覆盖分箱比其他目前主要基于序列组成的方法更有利于恢复更完整和更高保真度的基因组分箱。这种方法将是标准宏基因组工具包的重要补充，极大地提高了对未培养微生物基因组的获取。
