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Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis

Penington, Jocelyn Sietsma, Penno, Megan AS, Ngui, Katrina M, Ajami, Nadim J, Roth-Schulze, Alexandra J, Wilcox, Stephen A, Bandala-Sanchez, Esther, Wentworth, John M, Barry, Simon C, Brown, Cheryl Y, Couper, Jennifer J, Petrosino, Joseph F, Papenfuss, Anthony T, Harrison, Leonard C, Colman, PG, Cotterill, A, Craig, ME, Davis, EA, Harris, M, Haynes, A, Giles, L, Morahan, G, Morbey, C, Rawlinson, WD, Sinnott, RO, Soldatos, G, Thomson, RL and Vuillermin, Peter 2018, Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis, Scientific reports, vol. 8, pp. 1-9, doi: 10.1038/s41598-018-22491-7.

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Title Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis
Author(s) Penington, Jocelyn Sietsma
Penno, Megan AS
Ngui, Katrina M
Ajami, Nadim J
Roth-Schulze, Alexandra J
Wilcox, Stephen A
Bandala-Sanchez, Esther
Wentworth, John M
Barry, Simon C
Brown, Cheryl Y
Couper, Jennifer J
Petrosino, Joseph F
Papenfuss, Anthony T
Harrison, Leonard C
Colman, PG
Cotterill, A
Craig, ME
Davis, EA
Harris, M
Haynes, A
Giles, L
Morahan, G
Morbey, C
Rawlinson, WD
Sinnott, RO
Soldatos, G
Thomson, RL
Vuillermin, Peter
Journal name Scientific reports
Volume number 8
Article ID 4386
Start page 1
End page 9
Total pages 9
Publisher Nature Publishing Group
Place of publication London, Eng.
Publication date 2018-03-12
ISSN 2045-2322
Keyword(s) fecal sampling
gut microbiome
16S rRNA genes
DNA extraction
sequencing
Summary To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at-80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline. Variation in gut microbiome was dominated by differences between individuals. Minor differences in the abundance of taxa were found between collection-processing methods and day of collection, and between the two centers. We conclude that collection with storage and transport at 4 °C within 24 h is adequate for 16S rRNA analysis of the gut microbiome. Other factors including differences in PCR and sequencing methods account for relatively minor variation compared to differences between individuals.
Language eng
DOI 10.1038/s41598-018-22491-7
Copyright notice ©2018, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30110512

Document type: Journal Article
Collections: School of Medicine
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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.