Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, 4072, Australia.
Nat Microbiol. 2017 Nov;2(11):1533-1542. doi: 10.1038/s41564-017-0012-7. Epub 2017 Sep 11.
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.
培养微生物的挑战限制了现有微生物基因组的系统发育多样性。这一问题通过测序通量和计算技术的进步得到了解决，这些技术允许从宏基因组中进行无需培养的基因组回收。在这里，我们报告了从超过 1500 个公共宏基因组中重建了 7903 个细菌和古菌基因组。所有基因组的估计完整性均≥50%，近一半的基因组完整性≥90%，污染率≤5%。这些基因组将细菌和古菌系统发育树的多样性增加了>30%，并为 17 个细菌和 3 个古菌候选门提供了首个代表。我们还从 Patescibacteria 超门（也称为候选门辐射）中回收了 245 个基因组，发现该组的相对多样性随不同的蛋白质标记集而有很大差异。该数据集的规模和质量表明，从宏基因组中回收基因组为探索微生物暗物质提供了一条便捷的途径。
