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Enhancing Long-Read-Based Strain-Aware Metagenome Assembly

Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at...

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Autores principales: Luo, Xiao, Kang, Xiongbin, Schönhuth, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9136235/
https://www.ncbi.nlm.nih.gov/pubmed/35646097
http://dx.doi.org/10.3389/fgene.2022.868280
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author Luo, Xiao
Kang, Xiongbin
Schönhuth, Alexander
author_facet Luo, Xiao
Kang, Xiongbin
Schönhuth, Alexander
author_sort Luo, Xiao
collection PubMed
description Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition of microbial communities, the problem has largely remained unresolved so far. Next-generation sequencing has been routinely used in metagenome assembly but there have been struggles to generate strain-specific genome sequences due to the short-read length. This explains why long-read sequencing technologies have recently provided unprecedented opportunities to carry out haplotype- or strain-resolved genome assembly. Here, we propose MetaBooster and MetaBooster-HiFi, as two pipelines for strain-aware metagenome assembly from PacBio CLR and Oxford Nanopore long-read sequencing data. Benchmarking experiments on both simulated and real sequencing data demonstrate that either the MetaBooster or the MetaBooster-HiFi pipeline drastically outperforms the state-of-the-art de novo metagenome assemblers, in terms of all relevant metagenome assembly criteria, involving genome fraction, contig length, and error rates.
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spelling pubmed-91362352022-05-28 Enhancing Long-Read-Based Strain-Aware Metagenome Assembly Luo, Xiao Kang, Xiongbin Schönhuth, Alexander Front Genet Genetics Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition of microbial communities, the problem has largely remained unresolved so far. Next-generation sequencing has been routinely used in metagenome assembly but there have been struggles to generate strain-specific genome sequences due to the short-read length. This explains why long-read sequencing technologies have recently provided unprecedented opportunities to carry out haplotype- or strain-resolved genome assembly. Here, we propose MetaBooster and MetaBooster-HiFi, as two pipelines for strain-aware metagenome assembly from PacBio CLR and Oxford Nanopore long-read sequencing data. Benchmarking experiments on both simulated and real sequencing data demonstrate that either the MetaBooster or the MetaBooster-HiFi pipeline drastically outperforms the state-of-the-art de novo metagenome assemblers, in terms of all relevant metagenome assembly criteria, involving genome fraction, contig length, and error rates. Frontiers Media S.A. 2022-05-13 /pmc/articles/PMC9136235/ /pubmed/35646097 http://dx.doi.org/10.3389/fgene.2022.868280 Text en Copyright © 2022 Luo, Kang and Schönhuth. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Luo, Xiao
Kang, Xiongbin
Schönhuth, Alexander
Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
title Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
title_full Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
title_fullStr Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
title_full_unstemmed Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
title_short Enhancing Long-Read-Based Strain-Aware Metagenome Assembly
title_sort enhancing long-read-based strain-aware metagenome assembly
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9136235/
https://www.ncbi.nlm.nih.gov/pubmed/35646097
http://dx.doi.org/10.3389/fgene.2022.868280
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