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^*

^*この研究の対応する著者

研究成果 › 査読

374 被引用数 (Scopus)

抄録

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.

本文言語	English
ページ（範囲）	1069-1076
ページ数	8
ジャーナル	Nature Biotechnology
巻	35
号	11
DOI	https://doi.org/10.1038/nbt.3960
出版ステータス	Published - 2017 11月 1

ASJC Scopus subject areas

バイオテクノロジー
バイオエンジニアリング
応用微生物学とバイオテクノロジー
分子医療
生体医工学

UN SDG

この成果は、次の持続可能な開発目標に貢献しています

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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(11), 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, FE, 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, no. 11, 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 - Hattori, Masahira

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Towards standards for human fecal sample processing in metagenomic studies

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ASJC Scopus subject areas

UN SDG

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