Towards standards for human fecal sample processing in metagenomic studies
Paul I. Costea
,
Georg Zeller
,
Shinichi Sunagawa
,
Eric Pelletier
(1, 2)
,
Adriana A. 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
Paul I. Costea
- Function : Author
Georg Zeller
- Function : Author
Shinichi Sunagawa
- Function : Author
Eric Pelletier
- Function : Author
- PersonId : 183144
- IdHAL : eric
- ORCID : 0000-0003-4228-1712
- IdRef : 250792974
Adriana A. Alberti
- Function : Author
- PersonId : 183113
- IdHAL : adriana-alberti
- ORCID : 0000-0003-3372-9423
Melanie Tramontano
- Function : Author
Marja Driessen
- Function : Author
Rajna Hercog
- Function : Author
Ferris-Elias Jung
- Function : Author
Jens Roat Kultima
- Function : Author
Matthew R. Hayward
- Function : Author
Luis Pedro Coelho
- Function : Author
Emma Allen-Vercoe
- Function : Author
Michael Blaut
- Function : Author
Jillian R. M. Brown
- Function : Author
Thomas Carton
- Function : Author
- PersonId : 779975
- IdRef : 117998923
Stéphanie Cools-Portier
- Function : Author
Muriel Derrien
- Function : Author
Anne Druesne
- Function : Author
Willem M. De Vos
- Function : Author
B. Brett Finlay
- Function : Author
Harry J. Flint
- Function : Author
- 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
- Function : Author
- PersonId : 737756
- IdHAL : emmanuelle-le-chatelier
- ORCID : 0000-0002-2724-0536
Volker Mai
- Function : Author
Chaysavanh Manichanh
- Function : Author
Jennifer C. Martin
- Function : Author
Clémentine Mery
- Function : Author
Hidetoshi Morita
- Function : Author
Paul W. O'Toole
- Function : Author
Kiran Raosaheb Patil
- Function : Author
John Penders
- Function : Author
Søren Persson
- Function : Author
Milena Popova
- Function : Author
Anne Salonen
- Function : Author
Delphine Saulnier
- Function : Author
Karen P. Scott
- Function : Author
Bhagirath Singh
- Function : Author
Kathleen Slezak
- Function : Author
Patrick Veiga
- Function : Author
James Versalovic
- Function : Author
Liping Zhao
- Function : Author
Erwin G. Zoetendal
- Function : Author
Peer Bork
- Function : Author
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.