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Towards standards for human fecal sample processing in metagenomic studies

Item Type:Article
Title:Towards standards for human fecal sample processing in metagenomic studies
Creators Name:Costea, P.I. and Zeller, G. and Sunagawa, S. and Pelletier, E. and Alberti, A. and Levenez, F. and Tramontano, M. and Driessen, M. and Hercog, R. and Jung, F.E. and Kultima, J.R. and Hayward, M.R. and Coelho, L.P. and Allen-Vercoe, E. and Bertrand, L. and Blaut, M. and Brown, J.R.M. and Carton, T. and Cools-Portier, S. and Daigneault, M. and Derrien, M. and Druesne, A. and de Vos, W.M. and Finlay, B.B. and Flint, H.J. and Guarner, F. and Hattori, M. and Heilig, H. and Luna, R.A. and van Hylckama Vlieg, J. and Junick, J. and Klymiuk, I. and Langella, P. and Le Chatelier, Z. and Mai, V. and Manichanh, C. and Martin, J.C. and Mery, C. and Morita, H. and O'Toole, P.W. and Orvain, C. and Patil, K.R. and Penders, J. and Persson, S. and Pons, N. and Popova, M. and Salonen, A. and Saulnier, D. and Scott, K.P. and Singh, B. and Slezak, K. and Veiga, P. and Versalovic, J. and Zhao, L. and Zoetendal, E.G. and Ehrlich, S.D. and Dore, J. and Bork, P.
Abstract:Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
Keywords:Bacteria, Chemical Fractionation, Computational Biology, DNA, Feces, Metagenomics, Quality Control, Species Specificity
Source:Nature Biotechnology
ISSN:1087-0156
Publisher:Nature Publishing Group (U.S.A.)
Volume:35
Number:11
Page Range:1069-1076
Date:November 2017
Official Publication:https://doi.org/10.1038/nbt.3960
PubMed:View item in PubMed

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