| Literature DB >> 28967887 |
Paul I Costea1, Georg Zeller1, Shinichi Sunagawa1,2, Eric Pelletier3,4,5, Adriana Alberti3, Florence Levenez6, Melanie Tramontano1, Marja Driessen1, Rajna Hercog1, Ferris-Elias Jung1, Jens Roat Kultima1, Matthew R Hayward1, Luis Pedro Coelho1, Emma Allen-Vercoe7, Laurie Bertrand3, Michael Blaut8, Jillian R M Brown9, Thomas Carton10, Stéphanie Cools-Portier11, Michelle Daigneault6, Muriel Derrien11, Anne Druesne11, Willem M de Vos12,13, B Brett Finlay14, Harry J Flint15, Francisco Guarner16, Masahira Hattori17,18, Hans Heilig12, Ruth Ann Luna19, Johan van Hylckama Vlieg11, Jana Junick8, Ingeborg Klymiuk20, Philippe Langella6, Emmanuelle Le Chatelier6, Volker Mai21, Chaysavanh Manichanh16, Jennifer C Martin15, Clémentine Mery10, Hidetoshi Morita22, Paul W O'Toole9, Céline Orvain3, Kiran Raosaheb Patil1, John Penders23, Søren Persson24, Nicolas Pons6, Milena Popova10, Anne Salonen13, Delphine Saulnier8, Karen P Scott15, Bhagirath Singh25, Kathleen Slezak8, Patrick Veiga11, James Versalovic19, Liping Zhao26, Erwin G Zoetendal12, S Dusko Ehrlich6,27, Joel Dore6, Peer Bork1,28,29,30.
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.Entities:
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Year: 2017 PMID： 28967887 DOI： 10.1038/nbt.3960
Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908