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

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Date
2016-05-10
Authors
Hill, Cian J.
Brown, Jillian R. M.
Lynch, Denise B.
Jeffery, Ian B.
Ryan, C. Anthony
Ross, R. Paul
Stanton, Catherine
O'Toole, Paul W.
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BioMed Central
Published Version
10.1186/s40168-016-0164-3
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Abstract
Background: 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 (p
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Keywords
Microbiome , Microbiota , Storage , Methodology , Infant , Elderly , Gut microbiota , Extraction methods , Intestinal microbiota , Bacterial , Impact , Samples , Reads
Citation
Hill, 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/s40168-016-0164-3
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https://hdl.handle.net/10468/3395
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Microbiology - Journal Articles
APC Microbiome Ireland - Journal Articles
Paediatrics and Child Health - Journal Articles
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© 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.