Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes

Microbiome

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

【 图 表 】

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