Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.

中文翻译：

---

通过纳米孔选择性测序从复杂微生物组中富集稀有和未知物种的基因组

稀有物种是微生物群落的重要成员，但由于其丰度较低，检索其基因组很困难。ReadUntil (RU) 方法允许纳米孔设备实时选择性地对特定 DNA 分子进行测序，这为富集稀有物种提供了机会。尽管通过降低已知宿主序列（例如人类基因组）的测序深度来富集稀有物种具有鲁棒性，但在群落组成尚不清楚的环境样本中基于RU的稀有物种富集仍然存在差距，并且许多稀有物种已经公共数据库中的参考基因组较差或不完整。因此，我们在这里提出metaRUpore来克服这一挑战。当我们将metaRUpore应用于嗜热厌氧消化器（TAD）群落和人类肠道微生物群落时，它减少了高丰度种群的覆盖范围，并适度增加（~2倍）稀有类群的基因组覆盖范围，促进了近乎-完成了稀有物种的宏基因组组装基因组（nf-MAG）。该方法的简单性和稳健性使得具有中等计算资源的实验室可以使用它，并有可能成为未来复杂微生物组宏基因组测序的标准实践。