Qayyum Hajra, Talib Muhammad Sarfraz, Ali Amjad, Kayani Masood Ur Rehman
Integrative Biology Laboratory, Department of Microbiology and Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Srinagar Highway, Sector H-12, Islamabad, Pakistan.
Capital University of Science & Technology, Islamabad Expressway, Kahuta Road Zone-V Sihala, Islamabad, Pakistan.
Heliyon. 2025 Jan 14;11(2):e41938. doi: 10.1016/j.heliyon.2025.e41938. eCollection 2025 Jan 30.
Human-associated microbial communities are a complex mixture of bacterial species and diverse strains prevalent at varying abundances. Due to the inherent limitations of metagenomic assemblers and genome binning tools in recovering low-abundance species (<1 %) and strains, we lack comprehensive insight into these communities. Although many bioinformatics approaches are available for recovering metagenome-assembled genomes, their effectiveness in recovering low-abundance species and strains is often questioned. Moreover, each tool has its trade-offs, making selecting the right tools challenging. In this study, we investigated the combinatory effect of various assemblers and binning tools on the recovery of low-abundance species and strain-resolved genomes from real and simulated human metagenomes. We evaluated the performance of nine combinations of metagenome assemblers and genome binning tools for their potential to recover genomes of useable quality. Our results revealed that the metaSPAdes-MetaBAT2 combination is highly effective in recovering low-abundance species, while MEGAHIT-MetaBAT2 excels in recovering strain-resolved genomes. These findings highlight the significant variation in the performance of different combinations, even when aiming for the same objective. This suggests the profound impact of selecting the right assembler-binner combination for metagenome analyses. We believe this study will be a cornerstone for the scientific community, guiding the choice of tools by highlighting their complementary effects. Furthermore, it underscores the potential of existing tools to address the current challenges in the field improving the recovery of information from metagenomes.
与人类相关的微生物群落是细菌物种和各种菌株的复杂混合物，它们以不同的丰度普遍存在。由于宏基因组组装器和基因组分箱工具在恢复低丰度物种（<1%）和菌株方面存在固有限制，我们对这些群落缺乏全面的了解。尽管有许多生物信息学方法可用于恢复宏基因组组装的基因组，但它们在恢复低丰度物种和菌株方面的有效性常常受到质疑。此外，每个工具都有其权衡之处，这使得选择合适的工具具有挑战性。在本研究中，我们调查了各种组装器和分箱工具对从真实和模拟人类宏基因组中恢复低丰度物种和菌株解析基因组的组合效应。我们评估了九种宏基因组组装器和基因组分箱工具组合在恢复可用质量基因组方面的潜力。我们的结果表明，metaSPAdes-MetaBAT2组合在恢复低丰度物种方面非常有效，而MEGAHIT-MetaBAT2在恢复菌株解析基因组方面表现出色。这些发现突出了即使目标相同，不同组合的性能也存在显著差异。这表明选择合适的组装器-分箱器组合对宏基因组分析具有深远影响。我们相信这项研究将成为科学界的基石，通过突出其互补效应来指导工具的选择。此外，它强调了现有工具在应对该领域当前挑战方面的潜力，即提高从宏基因组中恢复信息的能力。
