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Towards standards for human fecal sample processing in metagenomic studies

Paul I. Costea Georg Zeller Shinichi Sunagawa Eric Pelletier 1, 2 Adriana Alberti 1 Florence Levenez 3 Melanie Tramontano Marja Driessen Rajna Hercog Ferris-Elias Jung Jens Roat Kultima Matthew R. Hayward Luis Pedro Coelho Emma Allen-Vercoe Laurie Bertrand 1 Michael Blaut Jillian R. M. Brown Thomas Carton Stéphanie Cools-Portier Michelle Daigneault 3 Muriel Derrien Anne Druesne Willem M. De Vos B. Brett Finlay Harry J. Flint Francisco Guarner Masahira Hattori Hans Heilig Ruth Ann Luna Johan van Hylckama Vlieg Jana Junick Ingeborg Klymiuk Philippe Langella 3 Emmanuelle Le Chatelier 3 Volker Mai Chaysavanh Manichanh Jennifer C. Martin Clémentine Mery Hidetoshi Morita Paul W. O'Toole Céline Orvain 1 Kiran Raosaheb Patil John Penders Søren Persson Nicolas Pons 3 Milena Popova Anne Salonen Delphine Saulnier Karen P. Scott Bhagirath Singh Kathleen Slezak Patrick Veiga James Versalovic Liping Zhao Erwin G. Zoetendal S. Dusko Ehrlich 3 Joel Dore 3 Peer Bork
1 JACOB - Institut de Biologie François JACOB
2 UMR 8030 - Génomique métabolique
3 MetaGenoPolis
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 : dna-extraction methods bacterial-dna diversity disease
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Journal articles
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https://hal-cea.archives-ouvertes.fr/cea-02073086
Contributor : Bruno Savelli Connect in order to contact the contributor
Submitted on : Tuesday, March 19, 2019 - 3:57:12 PM
Last modification on : Tuesday, September 7, 2021 - 3:36:24 PM

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CEA | CNRS | CEA-UPSAY | GENOMIQUE-METABOLIQUE | JACOB | CEA-DRF | UNIV-EVRY | INRA | GENOSCOPE | INRAE | GS-BIOSPHERA

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Paul I. Costea, Georg Zeller, Shinichi Sunagawa, Eric Pelletier, Adriana Alberti, et al.. Towards standards for human fecal sample processing in metagenomic studies. Nature Biotechnology, Nature Publishing Group, 2017, 35 (11), pp.1069-1076. ⟨10.1038/nbt.3960⟩. ⟨cea-02073086⟩

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