Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

ABSTRACT High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad...

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Autores principales:	Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Evguenia Kopylova, James T. Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke R. Thompson, Embriette R. Hyde, Antonio Gonzalez, Rob Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	DNA sequencing microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f271e73bcaa14332a1a9a8d045d81b4a
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spelling	oai:doaj.org-article:f271e73bcaa14332a1a9a8d045d81b4a2021-12-02T18:15:43ZDeblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns10.1128/mSystems.00191-162379-5077https://doaj.org/article/f271e73bcaa14332a1a9a8d045d81b4a2017-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00191-16https://doaj.org/toc/2379-5077ABSTRACT High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms. Deblur substantially reduces computational demands relative to similar sOTU methods and does so with similar or better sensitivity and specificity. Using simulations, mock mixtures, and real data sets, we detected closely related bacterial sequences with single nucleotide differences while removing false positives and maintaining stability in detection, suggesting that Deblur is limited only by read length and diversity within the amplicon sequences. Because Deblur operates on a per-sample level, it scales to modern data sets and meta-analyses. To highlight Deblur’s ability to integrate data sets, we include an interactive exploration of its application to multiple distinct sequencing rounds of the American Gut Project. Deblur is open source under the Berkeley Software Distribution (BSD) license, easily installable, and downloadable from https://github.com/biocore/deblur . IMPORTANCE Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose amplicons differ by a single base pair, is applicable in an automated fashion to large-scale sequencing data sets, and can integrate sequencing runs collected over time.Amnon AmirDaniel McDonaldJose A. Navas-MolinaEvguenia KopylovaJames T. MortonZhenjiang Zech XuEric P. KightleyLuke R. ThompsonEmbriette R. HydeAntonio GonzalezRob KnightAmerican Society for MicrobiologyarticleDNA sequencingmicrobiomeMicrobiologyQR1-502ENmSystems, Vol 2, Iss 2 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA sequencing microbiome Microbiology QR1-502
spellingShingle	DNA sequencing microbiome Microbiology QR1-502 Amnon Amir Daniel McDonald Jose A. Navas-Molina Evguenia Kopylova James T. Morton Zhenjiang Zech Xu Eric P. Kightley Luke R. Thompson Embriette R. Hyde Antonio Gonzalez Rob Knight Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
description	ABSTRACT High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms. Deblur substantially reduces computational demands relative to similar sOTU methods and does so with similar or better sensitivity and specificity. Using simulations, mock mixtures, and real data sets, we detected closely related bacterial sequences with single nucleotide differences while removing false positives and maintaining stability in detection, suggesting that Deblur is limited only by read length and diversity within the amplicon sequences. Because Deblur operates on a per-sample level, it scales to modern data sets and meta-analyses. To highlight Deblur’s ability to integrate data sets, we include an interactive exploration of its application to multiple distinct sequencing rounds of the American Gut Project. Deblur is open source under the Berkeley Software Distribution (BSD) license, easily installable, and downloadable from https://github.com/biocore/deblur . IMPORTANCE Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose amplicons differ by a single base pair, is applicable in an automated fashion to large-scale sequencing data sets, and can integrate sequencing runs collected over time.
format	article
author	Amnon Amir Daniel McDonald Jose A. Navas-Molina Evguenia Kopylova James T. Morton Zhenjiang Zech Xu Eric P. Kightley Luke R. Thompson Embriette R. Hyde Antonio Gonzalez Rob Knight
author_facet	Amnon Amir Daniel McDonald Jose A. Navas-Molina Evguenia Kopylova James T. Morton Zhenjiang Zech Xu Eric P. Kightley Luke R. Thompson Embriette R. Hyde Antonio Gonzalez Rob Knight
author_sort	Amnon Amir
title	Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
title_short	Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
title_full	Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
title_fullStr	Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
title_full_unstemmed	Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
title_sort	deblur rapidly resolves single-nucleotide community sequence patterns
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/f271e73bcaa14332a1a9a8d045d81b4a
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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

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