TY - JOUR
T1 - Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis
AU - ENDIA Study Group
AU - Penington, Jocelyn Sietsma
AU - Penno, Megan A.S.
AU - Ngui, Katrina M.
AU - Ajami, Nadim J.
AU - Roth-Schulze, Alexandra J.
AU - Wilcox, Stephen A.
AU - Bandala-Sanchez, Esther
AU - Wentworth, John M.
AU - Barry, Simon C.
AU - Brown, Cheryl Y.
AU - Couper, Jennifer J.
AU - Petrosino, Joseph F.
AU - Papenfuss, Anthony T.
AU - Harrison, Leonard C.
AU - Colman, Peter G.
AU - Cotterill, Andrew
AU - Craig, Maria E.
AU - Davis, Elizabeth A.
AU - Harris, Mark
AU - Haynes, Aveni
AU - Giles, Lynne
AU - Morahan, Grant
AU - Morbey, Claire
AU - Rawlinson, William D.
AU - Sinnott, Richard O.
AU - Soldatos, Georgia
AU - Thomson, Rebecca L.
AU - Vuillermin, Peter J.
PY - 2018/12/1
Y1 - 2018/12/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85044249093&partnerID=8YFLogxK
U2 - 10.1038/s41598-018-22491-7
DO - 10.1038/s41598-018-22491-7
M3 - Article
C2 - 29531234
AN - SCOPUS:85044249093
SN - 2045-2322
VL - 8
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 4386
ER -