Towards standards for human fecal sample processing in metagenomic studies - CEA - Commissariat à l’énergie atomique et aux énergies alternatives Access content directly
Journal Articles Nature Biotechnology Year : 2017

Towards standards for human fecal sample processing in metagenomic studies

Paul I. Costea
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Georg Zeller
  • Function : Author
Shinichi Sunagawa
  • Function : Author
Florence Levenez
  • Function : Author
Melanie Tramontano
  • Function : Author
Marja Driessen
  • Function : Author
Rajna Hercog
  • Function : Author
Ferris-Elias Jung
  • Function : Author
Jens Roat Kultima
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Matthew R. Hayward
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Luis Pedro Coelho
  • Function : Author
Emma Allen-Vercoe
  • Function : Author
Michael Blaut
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Jillian R. M. Brown
  • Function : Author
Thomas Carton
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  • PersonId : 779975
  • IdRef : 117998923
Stéphanie Cools-Portier
  • Function : Author
Muriel Derrien
  • Function : Author
Anne Druesne
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Willem M. De Vos
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B. Brett Finlay
  • Function : Author
Harry J. Flint
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  • PersonId : 958081
Francisco Guarner
  • Function : Author
Masahira Hattori
  • Function : Author
Hans Heilig
  • Function : Author
Ruth Ann Luna
  • Function : Author
Johan van Hylckama Vlieg
  • Function : Author
Jana Junick
  • Function : Author
Ingeborg Klymiuk
  • Function : Author
Emmanuelle Le Chatelier
Volker Mai
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Chaysavanh Manichanh
  • Function : Author
Jennifer C. Martin
  • Function : Author
Clémentine Mery
  • Function : Author
Hidetoshi Morita
  • Function : Author
Paul W. O'Toole
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Kiran Raosaheb Patil
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John Penders
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Søren Persson
  • Function : Author
Nicolas Pons
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Milena Popova
  • Function : Author
Anne Salonen
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Delphine Saulnier
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Karen P. Scott
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Bhagirath Singh
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Kathleen Slezak
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Patrick Veiga
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James Versalovic
  • Function : Author
Liping Zhao
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Erwin G. Zoetendal
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S. Dusko Ehrlich
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  • PersonId : 1203280
Joel Dore
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Peer Bork
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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.

Dates and versions

cea-02073086 , version 1 (19-03-2019)

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