Towards standards for human fecal sample processing in metagenomic studies

Paul I Costea; Georg Zeller; Shinichi Sunagawa; Eric Pelletier; Adriana Alberti; Florence Levenez; Melanie Tramontano; Marja Driessen; Rajna Hercog; Ferris-Elias Jung; Jens Roat Kultima; Matthew R Hayward; Luis Pedro Coelho; Emma Allen-Vercoe; Laurie Bertrand; Michael Blaut; Jillian R M Brown; Thomas Carton; Stéphanie Cools-Portier; Michelle Daigneault; 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; Emmanuelle Le Chatelier; Volker Mai; Chaysavanh Manichanh; Jennifer C Martin; Clémentine Mery; Hidetoshi Morita; Paul W O'Toole; Céline Orvain; Kiran Raosaheb Patil; John Penders; Søren Persson; Nicolas Pons; 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; Joel Dore; Peer Bork

doi:10.1038/nbt.3960

Towards standards for human fecal sample processing in metagenomic studies

Paul I Costea, Georg Zeller, Shinichi Sunagawa, Eric Pelletier, Adriana Alberti, Florence Levenez, Melanie Tramontano, Marja Driessen, Rajna Hercog, Ferris-Elias Jung, Jens Roat Kultima, Matthew R Hayward, Luis Pedro Coelho, Emma Allen-Vercoe, Laurie Bertrand, Michael Blaut, Jillian R M Brown, Thomas Carton, Stéphanie Cools-Portier, Michelle DaigneaultMuriel 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, Emmanuelle Le Chatelier, Volker Mai, Chaysavanh Manichanh, Jennifer C Martin, Clémentine Mery, Hidetoshi Morita, Paul W O'Toole, Céline Orvain, Kiran Raosaheb Patil, John Penders, Søren Persson, Nicolas Pons, 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, Joel Dore, Peer Bork

The Rowett Institute of Nutrition and Health

Research output: Contribution to journal › Article › peer-review

546 Citations (Scopus)

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.

Original language	English
Pages (from-to)	1069–1076
Number of pages	8
Journal	Nature Biotechnology
Volume	35
Early online date	2 Oct 2017
DOIs	https://doi.org/10.1038/nbt.3960
Publication status	Published - 2017

Bibliographical note

We thank S. Burz and K. Weizer for editing and web-posting the SOPs. We thank D. Ordonez and N.P. Gabrielli Lopez for advice on flow cytometry, which was provided by the Flow Cytometry Core Facility, EMBL. This study was funded by the European Community's Seventh Framework Programme via International Human Microbiome Standards (HEALTH-F4-2010-261376) grant. We also received support from Scottish Government Rural and Environmental Science and Analytical Services as well as from EMBL.

Keywords

applied microbiology
metagenomics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Costea, P. I., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, F.-E., Kultima, J. R., Hayward, M. R., Coelho, L. P., Allen-Vercoe, E., Bertrand, L., Blaut, M., Brown, J. R. M., Carton, T., Cools-Portier, S., ... Bork, P. (2017). Towards standards for human fecal sample processing in metagenomic studies. Nature Biotechnology, 35, 1069–1076. https://doi.org/10.1038/nbt.3960

Costea, PI, Zeller, G, Sunagawa, S, Pelletier, E, Alberti, A, Levenez, F, Tramontano, M, Driessen, M, Hercog, R, Jung, F-E, Kultima, JR, Hayward, MR, Coelho, LP, Allen-Vercoe, E, Bertrand, L, Blaut, M, Brown, JRM, Carton, T, Cools-Portier, S, Daigneault, M, Derrien, M, Druesne, A, de Vos, WM, Finlay, BB, Flint, HJ, Guarner, F, Hattori, M, Heilig, H, Luna, RA, van Hylckama Vlieg, J, Junick, J, Klymiuk, I, Langella, P, Le Chatelier, E, Mai, V, Manichanh, C, Martin, JC, Mery, C, Morita, H, O'Toole, PW, Orvain, C, Patil, KR, Penders, J, Persson, S, Pons, N, Popova, M, Salonen, A, Saulnier, D, Scott, KP, Singh, B, Slezak, K, Veiga, P, Versalovic, J, Zhao, L, Zoetendal, EG, Ehrlich, SD, Dore, J & Bork, P 2017, 'Towards standards for human fecal sample processing in metagenomic studies', Nature Biotechnology, vol. 35, pp. 1069–1076. https://doi.org/10.1038/nbt.3960

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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.",

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AU - Costea, Paul I

AU - Zeller, Georg

AU - Sunagawa, Shinichi

AU - Pelletier, Eric

AU - Alberti, Adriana

AU - Levenez, Florence

AU - Tramontano, Melanie

AU - Driessen, Marja

AU - Hercog, Rajna

AU - Jung, Ferris-Elias

AU - Kultima, Jens Roat

AU - Hayward, Matthew R

AU - Coelho, Luis Pedro

AU - Allen-Vercoe, Emma

AU - Bertrand, Laurie

AU - Blaut, Michael

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AU - Derrien, Muriel

AU - Druesne, Anne

AU - de Vos, Willem M

AU - Finlay, B Brett

AU - Flint, Harry J

AU - Guarner, Francisco

AU - Hattori, Masahira

AU - Heilig, Hans

AU - Luna, Ruth Ann

AU - van Hylckama Vlieg, Johan

AU - Junick, Jana

AU - Klymiuk, Ingeborg

AU - Langella, Philippe

AU - Le Chatelier, Emmanuelle

AU - Mai, Volker

AU - Manichanh, Chaysavanh

AU - Martin, Jennifer C

AU - Mery, Clémentine

AU - Morita, Hidetoshi

AU - O'Toole, Paul W

AU - Orvain, Céline

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AU - Persson, Søren

AU - Pons, Nicolas

AU - Popova, Milena

AU - Salonen, Anne

AU - Saulnier, Delphine

AU - Scott, Karen P

AU - Singh, Bhagirath

AU - Slezak, Kathleen

AU - Veiga, Patrick

AU - Versalovic, James

AU - Zhao, Liping

AU - Zoetendal, Erwin G

AU - Ehrlich, S Dusko

AU - Dore, Joel

AU - Bork, Peer

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Towards standards for human fecal sample processing in metagenomic studies

Abstract

Bibliographical note

Keywords

UN SDGs

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