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Editor's Pick Observation | Novel Systems Biology Techniques

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

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
Jack A. Gilbert, Editor
Amnon Amir
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Daniel McDonald
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Jose A. Navas-Molina
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
cDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
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Evguenia Kopylova
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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James T. Morton
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Zhenjiang Zech Xu
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Eric P. Kightley
bDepartment of Applied Mathematics, and Interdisciplinary Quantitative Biology Graduate Program, University of Colorado Boulder, Boulder, Colorado, USA
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Luke R. Thompson
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Embriette R. Hyde
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Antonio Gonzalez
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Rob Knight
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
cDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
dCenter for Microbiome Innovation, University of California San Diego, San Diego, California, USA
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Jack A. Gilbert
Argonne National Laboratory
Roles: Editor
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DOI: 10.1128/mSystems.00191-16
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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.

  • Copyright © 2017 Amir et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license .

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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
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
mSystems Mar 2017, 2 (2) e00191-16; DOI: 10.1128/mSystems.00191-16

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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
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
mSystems Mar 2017, 2 (2) e00191-16; DOI: 10.1128/mSystems.00191-16
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KEYWORDS

DNA sequencing
microbiome

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