论文标题
旨在完全表示宏基因组样品中的细菌含量
Towards complete representation of bacterial contents in metagenomic samples
论文作者
论文摘要
背景：在微生物组社区的元素组装中，我们可能认为，由于其更深层的覆盖范围，丰富的物种将更容易组装。但是，这种连接很少经过测试。我们通常不知道我们缺少多少丰富的物种，也没有恢复这些物种的方法。 结果：在这里，我们提出了基于K-MER的基于K-MER和16S基于RNA的方法来衡量元素组装的完整性。我们表明，即使使用PACBIO高保真（HIFI）读数，也通常不会组装丰富的物种，因为高应变多样性可能导致重叠群碎片。我们开发了一种新型算法来通过鉴定圆形组装子图来恢复丰富的元基因组组装基因组（MAG）。我们的算法无参考，并与标准的元基因组套筒补充。在14个实际数据集上进行了评估，它挽救了许多现有方法缺少的丰富物种。 结论：我们的工作强调了元基因组完整性的重要性，而元基因组完整性以前经常被忽略。我们的算法会产生更多的圆形磁磁，并将其移动更近于微生物组群落的完整表示。
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant species we are missing and do not have an approach to recover these species. Results: Here we proposed k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We showed that even with PacBio High-Fidelity (HiFi) reads, abundant species are often not assembled as high strain diversity may lead to fragmented contigs. We developed a novel algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Our algorithm is reference-free and complement to standard metagenome binning. Evaluated on 14 real datasets, it rescued many abundant species that would be missing with existing methods. Conclusions: Our work stresses the importance of metagenome completeness which is often overlooked before. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbiome communities.
