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Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes
BACKGROUND: The 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; h...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9716684/ https://www.ncbi.nlm.nih.gov/pubmed/36457010 http://dx.doi.org/10.1186/s40168-022-01415-8 |
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author | Liu, Lei Yang, Yu Deng, Yu Zhang, Tong |
author_facet | Liu, Lei Yang, Yu Deng, Yu Zhang, Tong |
author_sort | Liu, Lei |
collection | PubMed |
description | BACKGROUND: The 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. RESULTS: Here, 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. CONCLUSIONS: Our 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-022-01415-8. |
format | Online Article Text |
id | pubmed-9716684 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-97166842022-12-03 Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes Liu, Lei Yang, Yu Deng, Yu Zhang, Tong Microbiome Brief Report BACKGROUND: The 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. RESULTS: Here, 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. CONCLUSIONS: Our 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-022-01415-8. BioMed Central 2022-12-02 /pmc/articles/PMC9716684/ /pubmed/36457010 http://dx.doi.org/10.1186/s40168-022-01415-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Brief Report Liu, Lei Yang, Yu Deng, Yu Zhang, Tong Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes |
title | Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes |
title_full | Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes |
title_fullStr | Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes |
title_full_unstemmed | Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes |
title_short | Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes |
title_sort | nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes |
topic | Brief Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9716684/ https://www.ncbi.nlm.nih.gov/pubmed/36457010 http://dx.doi.org/10.1186/s40168-022-01415-8 |
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