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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-05-10

AUTHORS

Cian J. Hill, Jillian R. M. Brown, Denise B. Lynch, Ian B. Jeffery, C. Anthony Ryan, R. Paul Ross, Catherine Stanton, Paul W. O’Toole

ABSTRACT

BackgroundAlterations 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.ResultsUse 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 < 0.001). When the microbiota profiles were analysed at the operational taxonomic unit (OTU) level, three infant datasets in the study did not cluster together, while only one elderly dataset did not. The lower microbiota diversity of the infant gut microbiota compared to the elderly gut microbiota (p < 0.001) means that any alteration in the infant datasets has a proportionally larger effect.ConclusionsThe commercial storage vials appear to be suitable for high diversity microbiota samples, but may be less appropriate for lower diversity samples. Differences between fresh and stored samples mean that where storage is unavoidable, a consistent storage regime should be used. We would recommend extraction ideally within the first week of storage. More... »

PAGES

19

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s40168-016-0164-3

DOI

http://dx.doi.org/10.1186/s40168-016-0164-3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1024117908

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27160322


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98 number of diseases
99 older adults
100 operational taxonomic unit (OTU) level
101 phylogenetic composition
102 previous studies
103 processing methods
104 profile
105 proportion
106 proxy
107 quality
108 reduction
109 regime
110 relative proportions
111 samples
112 sampling
113 shearing
114 simple proxy
115 stool
116 stool storage
117 storage
118 storage regimes
119 storage vials
120 stored samples
121 study
122 test
123 transport
124 transport medium
125 unit level
126 urgent need
127 vials
128 week 1
129 weeks
130 weeks storage
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