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

Hdl Handle:
http://hdl.handle.net/10147/612343
Title:
Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants.
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
Citation:
Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. 2016, 4 (1):19 Microbiome
Publisher:
Microbiome
Journal:
Microbiome
Issue Date:
May-2016
URI:
http://hdl.handle.net/10147/612343
DOI:
10.1186/s40168-016-0164-3
PubMed ID:
27160322
Abstract:
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.; 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 < 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.; The 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.
Item Type:
Article
Language:
en
Description:
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.
Keywords:
MICROBIOLOGY; GASTROENTEROLOGY
ISSN:
2049-2618

Full metadata record

DC FieldValue Language
dc.contributor.authorHill, Cian Jen
dc.contributor.authorBrown, Jillian R Men
dc.contributor.authorLynch, Denise Ben
dc.contributor.authorJeffery, Ian Ben
dc.contributor.authorRyan, C Anthonyen
dc.contributor.authorRoss, R Paulen
dc.contributor.authorStanton, Catherineen
dc.contributor.authorO'Toole, Paul Wen
dc.date.accessioned2016-06-09T14:04:58Zen
dc.date.available2016-06-09T14:04:58Zen
dc.date.issued2016-05en
dc.identifier.citationEffect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. 2016, 4 (1):19 Microbiomeen
dc.identifier.issn2049-2618en
dc.identifier.pmid27160322en
dc.identifier.doi10.1186/s40168-016-0164-3en
dc.identifier.urihttp://hdl.handle.net/10147/612343en
dc.descriptionAlterations 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.en
dc.description.abstractAlterations 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.en
dc.description.abstractUse 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.en
dc.description.abstractThe 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.en
dc.language.isoenen
dc.publisherMicrobiomeen
dc.rightsArchived with thanks to Microbiomeen
dc.subjectMICROBIOLOGYen
dc.subjectGASTROENTEROLOGYen
dc.titleEffect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants.en
dc.typeArticleen
dc.identifier.journalMicrobiomeen

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