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

ENDIA Study Group, 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, Peter G. Colman, Andrew Cotterill, Maria E. Craig, Elizabeth A. Davis, Mark HarrisAveni Haynes, Lynne Giles, Grant Morahan, Claire Morbey, William D. Rawlinson, Richard O. Sinnott, Georgia Soldatos, Rebecca L. Thomson, Peter J. Vuillermin

Research output: Contribution to journalArticlepeer-review

34 Citations (Scopus)


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.

Original languageEnglish
Article number4386
JournalScientific Reports
Issue number1
Publication statusPublished - 1 Dec 2018


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