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Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing

Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species...

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Autores principales: Sun, Yuhong, Cheng, Zhanwen, Li, Xiang, Yang, Qing, Zhao, Bixi, Wu, Ziqi, Xia, Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10234302/
https://www.ncbi.nlm.nih.gov/pubmed/37041035
http://dx.doi.org/10.1101/gr.277266.122
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author Sun, Yuhong
Cheng, Zhanwen
Li, Xiang
Yang, Qing
Zhao, Bixi
Wu, Ziqi
Xia, Yu
author_facet Sun, Yuhong
Cheng, Zhanwen
Li, Xiang
Yang, Qing
Zhao, Bixi
Wu, Ziqi
Xia, Yu
author_sort Sun, Yuhong
collection PubMed
description Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.
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spelling pubmed-102343022023-10-01 Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing Sun, Yuhong Cheng, Zhanwen Li, Xiang Yang, Qing Zhao, Bixi Wu, Ziqi Xia, Yu Genome Res Methods Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes. Cold Spring Harbor Laboratory Press 2023-04 /pmc/articles/PMC10234302/ /pubmed/37041035 http://dx.doi.org/10.1101/gr.277266.122 Text en © 2023 Sun et al.; Published by Cold Spring Harbor Laboratory Press https://creativecommons.org/licenses/by-nc/4.0/This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) .
spellingShingle Methods
Sun, Yuhong
Cheng, Zhanwen
Li, Xiang
Yang, Qing
Zhao, Bixi
Wu, Ziqi
Xia, Yu
Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
title Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
title_full Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
title_fullStr Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
title_full_unstemmed Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
title_short Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
title_sort genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
topic Methods
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10234302/
https://www.ncbi.nlm.nih.gov/pubmed/37041035
http://dx.doi.org/10.1101/gr.277266.122
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