Towards standards for human fecal sample processing in metagenomic studies

被引：549

作者：

Costea, Paul I. ^{[1
]}

Zeller, Georg ^{[1
]}

Sunagawa, Shinichi ^{[1
,2
]}

Pelletier, Eric ^{[3
,4
,5
]}

Alberti, Adriana ^{[3
]}

Levenez, Florence ^{[6
]}

Tramontano, Melanie ^{[1
]}

Driessen, Marja ^{[1
]}

Hercog, Rajna ^{[1
]}

Jung, Ferris-Elias ^{[1
]}

Kultima, Jens Roat ^{[1
]}

Hayward, Matthew R. ^{[1
]}

Coelho, Luis Pedro ^{[1
]}

Allen-Vercoe, Emma ^{[7
]}

Bertrand, Laurie ^{[3
]}

Blaut, Michael ^{[8
]}

Brown, Jillian R. M. ^{[9
,10
]}

Carton, Thomas ^{[11
]}

Cools-Portier, Stephanie ^{[12
]}

Daigneault, Michelle ^{[6
]}

Derrien, Muriel ^{[12
]}

Druesne, Anne ^{[12
]}

de Vos, Willem M. ^{[13
,14
]}

Finlay, B. Brett ^{[15
]}

Flint, Harry J. ^{[16
]}

Guarner, Francisco ^{[17
]}

Hattori, Masahira ^{[18
,19
]}

Heilig, Hans ^{[13
]}

Luna, Ruth Ann ^{[20
]}

Vlieg, Johan van Hylckama ^{[12
]}

Junick, Jana ^{[8
]}

Klymiuk, Ingeborg ^{[21
]}

Langella, Philippe ^{[6
]}

Le Chatelier, Emmanuelle ^{[6
]}

Mai, Volker ^{[22
,23
]}

Manichanh, Chaysavanh ^{[17
]}

Martin, Jennifer C. ^{[16
]}

Mery, Clementine ^{[11
]}

Morita, Hidetoshi ^{[24
]}

O'Toole, Paul W. ^{[9
,10
]}

Orvain, Celine ^{[3
]}

Patil, Kiran Raosaheb ^{[1
]}

Penders, John ^{[25
,26
]}

Persson, Soren ^{[27
]}

Pons, Nicolas ^{[6
]}

Popova, Milena ^{[11
]}

Salonen, Anne ^{[14
]}

Saulnier, Delphine ^{[8
]}

Scott, Karen P. ^{[16
]}

Singh, Bhagirath ^{[28
,29
]}

机构：

[1] European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany

[2] ETH, Inst Microbiol, Dept Biol, Zurich, Switzerland

[3] CEA, Inst Francois Jacob Genoscope, Evry, France

[4] CNRS, UMR 8030, Evry, France

[5] Univ Evry Val dEssonne, Evry, France

[6] Metagenopolis, Inst Natl Rech Agron, Jouy En Josas, France

[7] Univ Guelph, Dept Mol & Cellular Biol, Guelph, ON, Canada

[8] German Inst Human Nutr Potsdam Rehbrucke, Dept Gastrointestinal Microbiol, Nuthetal, Germany

[9] Univ Coll Cork, Sch Microbiol, Cork, Ireland

[10] Univ Coll Cork, APC Microbiome Inst, Cork, Ireland

[11] Biofortis, Merieux NutriSci, Nantes, France

[12] Danone Nutricia Res, Palaiseau, France

[13] Wageningen Univ & Res, Lab Microbiol, Wageningen, Netherlands

[14] Univ Helsinki, Dept Bacteriol & Immunol, Immunobiol Res Program, Helsinki, Finland

[15] Univ British Columbia, Michael Smith Lab, Vancouver, BC, Canada

[16] Univ Aberdeen, Rowett Inst Nutr & Hlth, Aberdeen, Scotland

[17] Vall dHebron Res Inst, Digest Syst Res Unit, Barcelona, Spain

[18] Univ Tokyo, Grad Sch Frontier Sci, Tokyo, Chiba, Japan

[19] Waseda Univ, Grad Sch Adv Sci & Engn, Tokyo, Japan

[20] Texas Childrens Hosp, Feigin Ctr, Houston, TX 77030 USA

[21] Med Univ Graz, Ctr Med Res, Graz, Austria

[22] Univ Florida, Emerging Pathogens Inst, Dept Epidemiol, Coll Publ Hlth & Hlth Profess, Gainesville, FL USA

[23] Univ Florida, Emerging Pathogens Inst, Coll Med, Gainesville, FL USA

[24] Okayama Univ, Grad Sch Environm & Life Sci, Okayama, Japan

[25] Maastricht Univ, Med Ctr, Schl Nutr & Translat Res Metab NUTRIM, Maastricht, Netherlands

[26] Maastricht Univ, Med Ctr, Care & Publ Hlth Res Inst Caphri, Dept Med Microbiol, Maastricht, Netherlands

[27] Statens Serum Inst, Dept Bacteria Parasites & Fungi, Unit Foodborne Infect, Copenhagen, Denmark

[28] Univ Western Ontario, Ctr Human Immunol, Dept Microbiol & Immunol, London, ON, Canada

[29] Univ Western Ontario, Robarts Res Inst, London, ON, Canada

[30] Shanghai Jiao Tong Univ, Shanghai Ctr Syst Biomed, Minist Educ, Key Lab Syst Biomed, Shanghai, Peoples R China

[31] Guys Hosp, Kings Coll London, Ctr Host Microbiome Interact, Dent Inst,Cent Off, London, England

[32] Univ Wurzburg, Bioctr, Dept Bioinformat, Wurzburg, Germany

[33] Mol Med Partnership Unit, Heidelberg, Germany

[34] Max Delbruck Ctr Mol Med, Berlin, Germany

来源：

NATURE BIOTECHNOLOGY | 2017年 / 35卷 / 11期

关键词：

DNA-EXTRACTION METHODS; HUMAN GUT MICROBIOTA; BACTERIAL-DNA; DIVERSITY; DISEASE;

D O I：

10.1038/nbt.3960

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页码：1069 / +

页数：9

共 38 条

[1] Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens
Ariefdjohan, Merlin W.
Savaiano, Dennis A.
Nakatsu, Cindy H.
[J]. NUTRITION JOURNAL, 2010, 9
[2] Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome
Carroll, Ian M.
Ringel-Kulka, Tamar
Keku, Temitope O.
Chang, Young-Hyo
Packey, Christopher D.
Sartor, R. Balfour
Ringel, Yehuda
[J]. AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY, 2011, 301 (05): : G799 - G807
[3] A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples
Claassen, Shantelle
du Toit, Elloise
Kaba, Mamadou
Moodley, Clinton
Zar, Heather J.
Nicol, Mark P.
[J]. JOURNAL OF MICROBIOLOGICAL METHODS, 2013, 94 (02) : 103 - 110
[4] An ecological and evolutionary perspective on human-microbe mutualism and disease
Dethlefsen, Les
McFall-Ngai, Margaret
Relman, David A.
[J]. NATURE, 2007, 449 (7164) : 811 - 818
[5] Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
Dominguez-Bello, Maria G.
Costello, Elizabeth K.
Contreras, Monica
Magris, Magda
Hidalgo, Glida
Fierer, Noah
Knight, Rob
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (26) : 11971 - 11975
[6] Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
Forslund, Kristoffer
Hildebrand, Falk
Nielsen, Trine
Falony, Gwen
Le Chatelier, Emmanuelle
Sunagawa, Shinichi
Prifti, Edi
Vieira-Silva, Sara
Gudmundsdottir, Valborg
Pedersen, Helle Krogh
Arumugam, Manimozhiyan
Kristiansen, Karsten
Voigt, Anita Yvonne
Vestergaard, Henrik
Hercog, Rajna
Costea, Paul Igor
Kultima, Jens Roat
Li, Junhua
Jorgensen, Torben
Levenez, Florence
Dore, Joel
Nielsen, H. Bjorn
Brunak, Soren
Raes, Jeroen
Hansen, Torben
Wang, Jun
Ehrlich, S. Dusko
Bork, Peer
Pedersen, Oluf
[J]. NATURE, 2015, 528 (7581) : 262 - +
[7] Identifying personal microbiomes using metagenomic codes
Franzosa, Eric A.
Huang, Katherine
Meadow, James F.
Gevers, Dirk
Lemon, Katherine P.
Bohannan, Brendan J. M.
Huttenhower, Curtis
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (22) : E2930 - E2938
[8] Relating the metatranscriptome and metagenome of the human gut
Franzosa, Eric A.
Morgan, Xochitl C.
Segata, Nicola
Waldron, Levi
Reyes, Joshua
Earl, Ashlee M.
Giannoukos, Georgia
Boylan, Matthew R.
Ciulla, Dawn
Gevers, Dirk
Izard, Jacques
Garrett, Wendy S.
Chan, Andrew T.
Huttenhower, Curtis
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2014, 111 (22) : E2329 - E2338
[9] Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Gohl, Daryl M.
Vangay, Pajau
Garbe, John
MacLean, Allison
Hauge, Adam
Becker, Aaron
Gould, Trevor J.
Clayton, Jonathan B.
Johnson, Timothy J.
Hunter, Ryan
Knights, Dan
Beckman, Kenneth B.
[J]. NATURE BIOTECHNOLOGY, 2016, 34 (09) : 942 - +
[10] Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities
Henderson, Gemma
Cox, Faith
Kittelmann, Sandra
Miri, Vahideh Heidarian
Zethof, Michael
Noel, Samantha J.
Waghorn, Garry C.
Janssen, Peter H.
[J]. PLOS ONE, 2013, 8 (09):

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