Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

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dc.contributor.authorHill, Cian J.
dc.contributor.authorBrown, Jillian R. M.
dc.contributor.authorLynch, Denise B.
dc.contributor.authorJeffery, Ian B.
dc.contributor.authorRyan, C. Anthony
dc.contributor.authorRoss, R. Paul
dc.contributor.authorStanton, Catherine
dc.contributor.authorO'Toole, Paul W.
dc.contributor.funderDepartment of Agriculture, Food and the Marineen
dc.contributor.funderScience Foundation Irelanden
dc.date.accessioned2016-12-19T12:03:27Z
dc.date.available2016-12-19T12:03:27Z
dc.date.issued2016-05-10
dc.date.updated2016-12-19T11:53:14Z
dc.description.abstractBackground: Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biopsies. There is an urgent need for collection and transport media that would allow faecal sampling at distance from the processing laboratory, obviating the need for same-day DNA extraction recommended by previous studies of freezing and processing methods for stool. We compared the faecal bacterial DNA quality and apparent phylogenetic composition derived using a commercial kit for stool storage and transport (DNA Genotek OMNIgene GUT) with that of freshly extracted samples, 22 from infants and 20 from older adults. Results: Use of the storage vials increased the quality of extracted bacterial DNA by reduction of DNA shearing. When infant and elderly datasets were examined separately, no differences in microbiota composition were observed due to storage. When the two datasets were combined, there was a difference according to a Wilcoxon test in the relative proportions of Faecalibacterium, Sporobacter, Clostridium XVIII, and Clostridium XlVa after 1 week's storage compared to immediately extracted samples. After 2 weeks' storage, Bacteroides abundance was also significantly different, showing an apparent increase from week 1 to week 2. The microbiota composition of infant samples was more affected than that of elderly samples by storage, with significantly higher Spearman distances between paired freshly extracted and stored samples (pen
dc.description.sponsorshipDepartment of Agriculture, Food and Marine (10FDairy INFANTMET); Science Foundation Ireland (SFI/12/RC/2273)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationHill, C. J., Brown, J. R. M., Lynch, D. B., Jeffery, I. B., Ryan, C. A., Ross, R. P., Stanton, C. and O’Toole, P. W. (2016) 'Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants', Microbiome, 4(19), pp. 1-10. doi:10.1186/s40168-016-0164-3en
dc.identifier.doi10.1186/s40168-016-0164-3
dc.identifier.endpage10en
dc.identifier.issn2049-2618
dc.identifier.issued19en
dc.identifier.journaltitleMicrobiomeen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/3395
dc.identifier.volume4en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.rights© 2016, Hill et al. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectMicrobiomeen
dc.subjectMicrobiotaen
dc.subjectStorageen
dc.subjectMethodologyen
dc.subjectInfanten
dc.subjectElderlyen
dc.subjectGut microbiotaen
dc.subjectExtraction methodsen
dc.subjectIntestinal microbiotaen
dc.subjectBacterialen
dc.subjectImpacten
dc.subjectSamplesen
dc.subjectReadsen
dc.titleEffect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infantsen
dc.typeArticle (peer-reviewed)en
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