Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

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dc.contributor.author Claesson, Marcus J.
dc.contributor.author Wang, Qiong
dc.contributor.author O'Sullivan, Orla
dc.contributor.author Greene-Diniz, Rachel
dc.contributor.author Cole, James R.
dc.contributor.author Ross, R. Paul
dc.contributor.author O'Toole, Paul W.
dc.date.accessioned 2017-11-14T13:24:31Z
dc.date.available 2017-11-14T13:24:31Z
dc.date.issued 2010
dc.identifier.citation Claesson, M. J., Wang, Q., O'Sullivan, O., Greene-Diniz, R., Cole, J. R., Ross, R. P. and O'Toole, P. W. (2010) 'Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions', Nucleic Acids Research, 38(22), e200 (13pp). doi: 10.1093/nar/gkq873 en
dc.identifier.volume 38
dc.identifier.issued 22
dc.identifier.startpage 1
dc.identifier.endpage 13
dc.identifier.issn 0305-1048
dc.identifier.issn 1362-4962
dc.identifier.uri http://hdl.handle.net/10468/5027
dc.identifier.doi 10.1093/nar/gkq873
dc.description.abstract High-throughput molecular technologies can profile microbial communities at high resolution even in complex environments like the intestinal microbiota. Recent improvements in next-generation sequencing technologies allow for even finer resolution. We compared phylogenetic profiling of both longer (454 Titanium) sequence reads with shorter, but more numerous, paired-end reads (Illumina). For both approaches, we targeted six tandem combinations of 16S rRNA gene variable regions, in microbial DNA extracted from a human faecal sample, in order to investigate their limitations and potentials. In silico evaluations predicted that the V3/V4 and V4/V5 regions would provide the highest classification accuracies for both technologies. However, experimental sequencing of the V3/V4 region revealed significant amplification bias compared to the other regions, emphasising the necessity for experimental validation of primer pairs. The latest developments of 454 and Illumina technologies offered higher resolution compared to their previous versions, and showed relative consistency with each other. However, the majority of the Illumina reads could not be classified down to genus level due to their shorter length and higher error rates beyond 60 nt. Nonetheless, with improved quality and longer reads, the far greater coverage of Illumina promises unparalleled insights into highly diverse and complex environments such as the human gut. en
dc.description.sponsorship US Department of Agriculture (USDA) National Institute of Food and Agriculture (National Research Initiative (2008-35107-04542) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press en
dc.relation.uri https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq873
dc.rights © 2010, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. en
dc.rights.uri http://creativecommons.org/licenses/by-nc/2.5
dc.subject Rare biosphere en
dc.subject Diversity en
dc.subject Primers en
dc.title Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Marcus J. Claesson, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: m.claesson@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Department of Agriculture, Food and the Marine
dc.contributor.funder U.S. Department of Agriculture
dc.contributor.funder Health Research Board
dc.description.status Peer reviewed en
dc.identifier.journaltitle Nucleic Acids Research en
dc.internal.IRISemailaddress m.claesson@ucc.ie en
dc.identifier.articleid e200


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© 2010, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Except where otherwise noted, this item's license is described as © 2010, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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