Towards standards for human fecal sample processing in metagenomic studies

被引：577

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

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