The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations

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dc.contributor.author Fouhy, Fiona
dc.contributor.author Deane, Jennifer
dc.contributor.author Rea, Mary C.
dc.contributor.author O'Sullivan, Orla
dc.contributor.author Ross, R. Paul
dc.contributor.author O'Callaghan, Grace
dc.contributor.author Plant, Barry J.
dc.contributor.author Stanton, Catherine
dc.date.accessioned 2016-02-17T10:07:59Z
dc.date.available 2016-02-17T10:07:59Z
dc.date.issued 2015
dc.identifier.citation Fouhy F, Deane J, Rea MC, O’Sullivan Ó, Ross RP, O’Callaghan G, et al. (2015) The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations. PLoS ONE 10(3): e0119355. doi:10.1371/journal.pone.0119355
dc.identifier.volume 10 en
dc.identifier.issued 3 en
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10468/2315
dc.identifier.doi 10.1371/journal.pone.0119355
dc.description.abstract Background: High-throughput sequencing has enabled detailed insights into complex microbial environments, including the human gut microbiota. The accuracy of the sequencing data however, is reliant upon appropriate storage of the samples prior to DNA extraction. The aim of this study was to conduct the first MiSeq sequencing investigation into the effects of faecal storage on the microbiota, compared to fresh samples. Culture-based analysis was also completed. Methods: Seven faecal samples were collected from healthy adults. Samples were separated into fresh (DNA extracted immediately), snap frozen on dry ice and frozen for 7 days at -80 degrees C prior to DNA extraction or samples frozen at -80 degrees C for 7 days before DNA extraction. Sequencing was completed on the Illumina MiSeq platform. Culturing of total aerobes, anaerobes and bifidobacteria was also completed. Results: No significant differences at phylum or family levels between the treatment groups occurred. At genus level only Faecalibacterium and Leuconostoc were significantly different in the fresh samples compared to the snap frozen group (p = 0.0298; p = 0.0330 respectively). Diversity analysis indicated that samples clustered based on the individual donor, rather than by storage group. No significant differences occurred in the culture-based analysis between the fresh, snap or -80 degrees C frozen samples. Conclusions: Using the MiSeq platform coupled with culture-based analysis, this study highlighted that limited significant changes in microbiota occur following rapid freezing of faecal samples prior to DNA extraction. Thus, rapid freezing of samples prior to DNA extraction and culturing, preserves the integrity of the microbiota. en
dc.description.sponsorship Teagasc (Walsh Fellowship); Science Foundation Ireland (SFI-CSET02/CE/B124; SFI/12/RC/2273); European Commission (FP7 Grant Agreement No. 603038); en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Public Library of Science en
dc.rights © 2015 Fouhy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en
dc.subject Gut microbiota en
dc.subject Storage conditions en
dc.subject Dna extraction en
dc.subject Bacterial en
dc.subject Samples en
dc.subject Collection en
dc.subject Diversity en
dc.subject Disease en
dc.subject Flora en
dc.title The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Paul Ross, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland. +353-21-490-3000 Email: p.ross@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.wokid WOS:000350689400068
dc.contributor.funder Teagasc
dc.contributor.funder Science Foundation Ireland
dc.contributor.funder European Commission
dc.description.status Peer reviewed en
dc.identifier.journaltitle PLOS ONE en
dc.internal.IRISemailaddress p.ross@ucc.ie en
dc.identifier.articleid e0119355


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© 2015 Fouhy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Except where otherwise noted, this item's license is described as © 2015 Fouhy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
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