Microbiome | |
Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes | |
Brief Report | |
Lei Liu1  Yu Yang1  Yu Deng1  Tong Zhang1  | |
[1] Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China; | |
关键词: Nanopore sequencing; Long-read metagenomics; Activated sludge microbiome; Reference-quality genome reconstruction; NanoPhase; Prophage; | |
DOI : 10.1186/s40168-022-01415-8 | |
received in 2022-06-07, accepted in 2022-11-07, 发布年份 2022 | |
来源: Springer | |
【 摘 要 】
BackgroundThe accurate and comprehensive analyses of genome-resolved metagenomics largely depend on the reconstruction of reference-quality (complete and high-quality) genomes from diverse microbiomes. Closing gaps in draft genomes have been approaching with the inclusion of Nanopore long reads; however, genome quality improvement requires extensive and time-consuming high-accuracy short-read polishing.ResultsHere, we introduce NanoPhase, an open-source tool to reconstruct reference-quality genomes from complex metagenomes using only Nanopore long reads. Using Kit 9 and Q20+ chemistries, we first evaluated the feasibility of NanoPhase using a ZymoBIOMICS gut microbiome standard (including 21 strains), then sequenced the complex activated sludge microbiome and reconstructed 275 MAGs with median completeness of ~ 90%. As a result, NanoPhase improved the MAG contiguity (median MAG N50: 735 Kb, 44-86X compared to conventional short-read-based methods) while maintaining high accuracy, allowing for a full and accurate investigation of target microbiomes. Additionally, leveraging these high-contiguity reference-quality genomes, we identified 165 prophages within 111 MAGs, with 5 as active prophages, indicating the prophage was a neglected source of genetic diversity within microbial populations and influencer in shaping microbial composition in the activated sludge microbiome.ConclusionsOur results demonstrated that NanoPhase enables reference-quality genome reconstruction from complex metagenomes directly using only Nanopore long reads. Furthermore, besides the 16S rRNA genes and biosynthetic gene clusters, the generated high-accuracy and high-contiguity MAGs improved the host identification of critical mobile genetic elements, e.g., prophage, serving as a genomic blueprint to investigate the microbial potential and ecology in the activated sludge ecosystem.BpjLD_tCw1wYtiRUQK79qoVideo Abstract
【 授权许可】
CC BY
© The Author(s) 2022
【 预 览 】
Files | Size | Format | View |
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RO202305061596213ZK.pdf | 4815KB | download | |
Fig. 1 | 284KB | Image | download |
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Fig. 11 | 97KB | Image | download |
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