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Type: Journal article
Title: Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis
Author: Penington, J.
Penno, M.
Ngui, K.
Ajami, N.
Roth-Schulze, A.
Wilcox, S.
Bandala-Sanchez, E.
Wentworth, J.
Barry, S.
Brown, C.
Couper, J.
Petrosino, J.
Papenfuss, A.
Harrison, L.
ENDIA Study Group
Colman, P.
Cotterill, A.
Craig, M.
Davis, E.
Harris, M.
et al.
Citation: Scientific Reports, 2018; 8(1):4386-1-4386-10
Publisher: Nature Publishing Group
Issue Date: 2018
ISSN: 2045-2322
Statement of
Jocelyn Sietsma Penington, Megan A. S. Penno, Katrina M. Ngui, Nadim J. Ajami, Alexandra J. Roth-Schulze, Stephen A. Wilcox, Esther Bandala-Sanchez, John M. Wentworth, Simon C. Barry, Cheryl Y. Brown, Jennifer J. Couper, Joseph F. Petrosino, Anthony T. Papenfuss, Leonard C. Harrison and ENDIA Study Group (Lynne Giles and Rebecca L. Thomson)
Abstract: 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.
Keywords: ENDIA Study Group*
Description: Published online: 12 March 2018
Rights: © The Author(s) 2018. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
DOI: 10.1038/s41598-018-22491-7
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Appears in Collections:Aurora harvest 3
Paediatrics publications

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