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 & 38 others 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

Research output: Contribution to journalArticle

79 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 languageEnglish
Pages (from-to)1069–1076
Number of pages8
JournalNature Biotechnology
Volume35
Early online date2 Oct 2017
DOIs
Publication statusPublished - 2017

Fingerprint

Metagenomics
DNA
Processing
Microbiota
Gram-Negative Bacteria
Chemical analysis
Libraries
Meta-Analysis
Bacteria
Health

Keywords

  • applied microbiology
  • metagenomics

Cite this

Costea, P. I., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., ... 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

Towards standards for human fecal sample processing in metagenomic studies. / Costea, Paul I; Zeller, Georg; Sunagawa, Shinichi; Pelletier, Eric; Alberti, Adriana; Levenez, Florence; Tramontano, Melanie; Driessen, Marja; Hercog, Rajna; Jung, Ferris-Elias; Kultima, Jens Roat; Hayward, Matthew R; Coelho, Luis Pedro; Allen-Vercoe, Emma; Bertrand, Laurie; Blaut, Michael; Brown, Jillian R M; Carton, Thomas; Cools-Portier, Stéphanie; Daigneault, Michelle; Derrien, Muriel; Druesne, Anne; de Vos, Willem M; Finlay, B Brett; Flint, Harry J; Guarner, Francisco; Hattori, Masahira; Heilig, Hans; Luna, Ruth Ann; van Hylckama Vlieg, Johan; Junick, Jana; Klymiuk, Ingeborg; Langella, Philippe; Le Chatelier, Emmanuelle; Mai, Volker; Manichanh, Chaysavanh; Martin, Jennifer C; Mery, Clémentine; Morita, Hidetoshi; O'Toole, Paul W; Orvain, Céline; Patil, Kiran Raosaheb; Penders, John; Persson, Søren; Pons, Nicolas; Popova, Milena; Salonen, Anne; Saulnier, Delphine; Scott, Karen P; Singh, Bhagirath; Slezak, Kathleen; Veiga, Patrick; Versalovic, James; Zhao, Liping; Zoetendal, Erwin G; Ehrlich, S Dusko; Dore, Joel; Bork, Peer.

In: Nature Biotechnology, Vol. 35, 2017, p. 1069–1076.

Research output: Contribution to journalArticle

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
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F et al. Towards standards for human fecal sample processing in metagenomic studies. Nature Biotechnology. 2017;35:1069–1076. https://doi.org/10.1038/nbt.3960
Costea, Paul I ; Zeller, Georg ; Sunagawa, Shinichi ; Pelletier, Eric ; Alberti, Adriana ; Levenez, Florence ; Tramontano, Melanie ; Driessen, Marja ; Hercog, Rajna ; Jung, Ferris-Elias ; Kultima, Jens Roat ; Hayward, Matthew R ; Coelho, Luis Pedro ; Allen-Vercoe, Emma ; Bertrand, Laurie ; Blaut, Michael ; Brown, Jillian R M ; Carton, Thomas ; Cools-Portier, Stéphanie ; Daigneault, Michelle ; Derrien, Muriel ; Druesne, Anne ; de Vos, Willem M ; Finlay, B Brett ; Flint, Harry J ; Guarner, Francisco ; Hattori, Masahira ; Heilig, Hans ; Luna, Ruth Ann ; van Hylckama Vlieg, Johan ; Junick, Jana ; Klymiuk, Ingeborg ; Langella, Philippe ; Le Chatelier, Emmanuelle ; Mai, Volker ; Manichanh, Chaysavanh ; Martin, Jennifer C ; Mery, Clémentine ; Morita, Hidetoshi ; O'Toole, Paul W ; Orvain, Céline ; Patil, Kiran Raosaheb ; Penders, John ; Persson, Søren ; Pons, Nicolas ; Popova, Milena ; Salonen, Anne ; Saulnier, Delphine ; Scott, Karen P ; Singh, Bhagirath ; Slezak, Kathleen ; Veiga, Patrick ; Versalovic, James ; Zhao, Liping ; Zoetendal, Erwin G ; Ehrlich, S Dusko ; Dore, Joel ; Bork, Peer. / Towards standards for human fecal sample processing in metagenomic studies. In: Nature Biotechnology. 2017 ; Vol. 35. pp. 1069–1076.
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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 - Mery, Clémentine

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