Reporting guidelines for human microbiome research: the STORMS checklist

被引：258

作者：

Mirzayi, Chloe ^{[1
]}

Renson, Audrey ^{[2
]}

Zohra, Fatima ^{[1
]}

Elsafoury, Shaimaa ^{[1
]}

Geistlinger, Ludwig ^{[1
]}

Kasselman, Lora J. ^{[1
]}

Eckenrode, Kelly ^{[1
]}

van de Wijgert, Janneke ^{[3
]}

Loughman, Amy ^{[4
]}

Marques, Francine Z. ^{[5
]}

MacIntyre, David A. ^{[6
]}

Arumugam, Manimozhiyan ^{[7
]}

Azhar, Rimsha ^{[1
]}

Beghini, Francesco ^{[8
]}

Bergstrom, Kirk ^{[9
]}

Bhatt, Ami ^{[10
,11
,12
]}

Bisanz, Jordan E. ^{[13
]}

Braun, Jonathan ^{[14
]}

Bravo, Hector Corrada ^{[15
]}

Buck, Gregory A. ^{[16
]}

Bushman, Frederic ^{[17
]}

Casero, David ^{[18
]}

Clarke, Gerard ^{[19
,20
]}

Carmen Collado, Maria ^{[21
]}

Cotter, Paul D. ^{[20
,22
,23
]}

Cryan, John F. ^{[20
,24
]}

Demmer, Ryan T. ^{[25
]}

Devkota, Suzanne ^{[18
]}

Elinav, Eran ^{[26
,27
]}

Escobar, Juan S. ^{[28
]}

Fettweis, Jennifer ^{[16
]}

Finn, Robert D. ^{[29
]}

Fodor, Anthony A. ^{[30
]}

Forslund, Sofia ^{[31
,32
]}

Franke, Andre ^{[33
]}

Furlanello, Cesare ^{[34
]}

Gilbert, Jack ^{[35
,36
]}

Grice, Elizabeth ^{[37
]}

Haibe-Kains, Benjamin ^{[38
]}

Handley, Scott ^{[39
]}

Herd, Pamela ^{[40
]}

Holmes, Susan ^{[41
]}

Jacobs, Jonathan P. ^{[42
]}

Karstens, Lisa ^{[43
]}

Knight, Rob ^{[44
]}

Knights, Dan ^{[45
,46
]}

Koren, Omry ^{[47
]}

Kwon, Douglas S. ^{[48
]}

Langille, Morgan ^{[49
]}

Lindsay, Brianna ^{[50
]}

机构：

[1] CUNY, Inst Implementat Sci Publ Hlth, Grad Sch Publ Hlth & Hlth Policy, New York, NY 10021 USA

[2] Univ N Carolina, Chapel Hill, NC 27515 USA

[3] Univ Utrecht, Univ Med Ctr Utrecht, Julius Ctr Hlth Sci & Primary Care, Utrecht, Netherlands

[4] Deakin Univ, Food & Mood Ctr, Inst Mental & Phys Hlth & Clin Translat, Geelong, Vic, Australia

[5] Monash Univ, Fac Sci, Sch Biol Sci, Hypertens Res Lab, Melbourne, Vic, Australia

[6] Imperial Coll London, Fac Med, Dept Metab Digest & Reprod, London, England

[7] Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metab Res, Fac Hlth & Med Sci, Copenhagen, Denmark

[8] Univ Trento, Dept CIBIO, Trento, Italy

[9] Univ British Columbia, Dept Biol, Okanagan Campus, Kelowna, BC, Canada

[10] Stanford Univ, Dept Med, Div Hematol, Stanford, CA 94305 USA

[11] Stanford Univ, Dept Med, Div Bone Marrow Transplantat, Stanford, CA 94305 USA

[12] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[13] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA

[14] Cedars Sinai Med Ctr, Dept Med, Div Gastroenterol & Hepatol, Los Angeles, CA 90048 USA

[15] Genentech Inc, San Francisco, CA 94080 USA

[16] Virginia Commonwealth Univ, Dept Microbiol & Immunol, Ctr Microbiome Engn & Data Anal, Richmond, VA 23298 USA

[17] Univ Penn, Philadelphia, PA 19104 USA

[18] Cedars Sinai Med Ctr, F Widjaja Fdn Inflammatory Bowel & Immunobiol Res, Los Angeles, CA 90048 USA

[19] Univ Coll Cork, Dept Psychiat & Neurobehav Sci, Cork, Ireland

[20] Univ Coll Cork, APC Microbiome Ireland, Cork, Ireland

[21] Inst Agrochem & Food Technol Natl Res Council, Valencia, Spain

[22] TEAGASC, Food Res Ctr Moorepk, Cork, Ireland

[23] VistaMilk, Cork, Ireland

[24] Univ Coll Cork, Dept Anat & Neurosci, Cork, Ireland

[25] Univ Minnesota, Sch Publ Hlth, Minneapolis, MN USA

[26] Weizmann Inst Sci, Immunol Dept, Rehovot, Israel

[27] Deutsch Krebsforschungszentrum, Microbiome & Canc Div, Heidelberg, Germany

[28] Grp Empresarial Nutresa, Vidarium Nutr Hlth & Wellness Res Ctr, Medellin, Colombia

[29] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Hinxton, England

[30] Univ N Carolina, Dept Bioinformat & Genom, Charlotte, NC USA

[31] Max Delbruck Ctr Mol Med, Expt & Clin Res Ctr, Berlin, Germany

[32] Charite, Berlin, Germany

[33] Univ Kiel, Inst Clin Mol Biol, Kiel, Germany

[34] HK3 Lab, Rovereto, Italy

[35] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA

[36] Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 USA

[37] Univ Penn, Dept Dermatol, Perelman Sch Med, Philadelphia, PA 19104 USA

[38] Univ Hlth Network, Princess Margaret Canc Ctr, Toronto, ON, Canada

[39] Washington Univ, Sch Med, Dept Pathol & Immunol, St Louis, MO USA

[40] Georgetown Univ, McCourt Sch Publ Policy, Washington, DC USA

[41] Stanford Univ, Dept Stat, Stanford, CA 94305 USA

[42] Univ Calif Los Angeles, David Geffen Sch Med, Div Digest Dis, Los Angeles, CA USA

[43] Oregon Hlth & Sci Univ, Dept Med Informat & Clin Epidemiol, Portland, OR 97201 USA

[44] Univ Calif San Diego, Ctr Microbiome Innovat, La Jolla, CA 92093 USA

[45] Univ Minnesota, Dept Comp Sci & Engn, Minneapolis, MN USA

[46] Univ Minnesota, Biotechnol Inst, St Paul, MN 55108 USA

[47] Bar Ilan Univ, Azrieli Fac Med, Safed, Israel

[48] Massachusetts Gen Hosp, Div Infect Dis, Boston, MA 02114 USA

[49] Dalhousie Univ, Dept Pharmacol, Halifax, NS, Canada

[50] Univ Maryland, Sch Med, Inst Human Virol, Baltimore, MD 21201 USA

来源：

NATURE MEDICINE | 2021年 / 27卷 / 11期

基金：

英国生物技术与生命科学研究理事会; 美国国家卫生研究院;

关键词：

GENETIC ASSOCIATION; CAUSAL INFERENCE; EXTENSION; QUALITY; STATEMENT; TRIALS; NULL;

D O I：

10.1038/s41591-021-01552-x

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results. The STORMS tool provides guidance for concise and complete reporting of microbiome studies to facilitate manuscript preparation, peer review, reader comprehension of publications, and comparative analysis of published results.

引用

页码：1885 / 1892

页数：8

共 49 条

[1] Challenges in the construction of knowledge bases for human microbiome-disease associations [J].

Badal, Varsha Dave ;

Wright, Dustin ;

Katsis, Yannis ;

Kim, Ho-Cheol ;

Swafford, Austin D. ;

Knight, Rob ;

Hsu, Chun-Nan .

MICROBIOME, 2019, 7 (01)

[2] STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies [J].

Bharucha, Tehmina ;

Oeser, Clarissa ;

Balloux, Francois ;

Brown, Julianne R. ;

Carbo, Ellen C. ;

Charlett, Andre ;

Chiu, Charles Y. ;

Claas, Eric C. J. ;

de Goffau, Marcus C. ;

de Vries, Jutte J. C. ;

Eloit, Marc ;

Hopkins, Susan ;

Huggett, Jim F. ;

MacCannell, Duncan ;

Morfopoulou, Sofia ;

Nath, Avindra ;

O'Sullivan, Denise M. ;

Reoma, Lauren B. ;

Shaw, Liam P. ;

Sidorov, Igor ;

Simner, Patricia J. ;

Tan, Le Van ;

Thomson, Emma C. ;

van Dorp, Lucy ;

Wilson, Michael R. ;

Breuer, Judith ;

Field, Nigel .

LANCET INFECTIOUS DISEASES, 2020, 20 (10) :E251-E260

[3]

Chen C., 2020, Gigabyte, V2020, P1, DOI [10.46471/gigabyte.9, DOI 10.46471/GIGABYTE.9]

[4] Gene expression profiling gut microbiota in different races of humans [J].

Chen, Lei ;

Zhang, Yu-Hang ;

Huang, Tao ;

Cai, Yu-Dong .

SCIENTIFIC REPORTS, 2016, 6

[5] Illustrating bias due to conditioning on a collider [J].

Cole, Stephen R. ;

Platt, Robert W. ;

Schisterman, Enrique F. ;

Chu, Haitao ;

Westreich, Daniel ;

Richardson, David ;

Poole, Charles .

INTERNATIONAL JOURNAL OF EPIDEMIOLOGY, 2010, 39 (02) :417-420

[6] Towards standards for human fecal sample processing in metagenomic studies [J].

Costea, Paul I. ;

Zeller, Georg ;

Sunagawa, Shinichi ;

Pelletier, Eric ;

Alberti, Adriana ;

Levenez, Florence ;

Tramontano, Melanie ;

Driessen, Marja ;

Hercog, Rajna ;

Jung, Ferris-Elias ;

Kultima, Jens Roat ;

Hayward, Matthew R. ;

Coelho, Luis Pedro ;

Allen-Vercoe, Emma ;

Bertrand, Laurie ;

Blaut, Michael ;

Brown, Jillian R. M. ;

Carton, Thomas ;

Cools-Portier, Stephanie ;

Daigneault, Michelle ;

Derrien, Muriel ;

Druesne, Anne ;

de Vos, Willem M. ;

Finlay, B. Brett ;

Flint, Harry J. ;

Guarner, Francisco ;

Hattori, Masahira ;

Heilig, Hans ;

Luna, Ruth Ann ;

Vlieg, Johan van Hylckama ;

Junick, Jana ;

Klymiuk, Ingeborg ;

Langella, Philippe ;

Le Chatelier, Emmanuelle ;

Mai, Volker ;

Manichanh, Chaysavanh ;

Martin, Jennifer C. ;

Mery, Clementine ;

Morita, Hidetoshi ;

O'Toole, Paul W. ;

Orvain, Celine ;

Patil, Kiran Raosaheb ;

Penders, John ;

Persson, Soren ;

Pons, Nicolas ;

Popova, Milena ;

Salonen, Anne ;

Saulnier, Delphine ;

Scott, Karen P. ;

Singh, Bhagirath .

NATURE BIOTECHNOLOGY, 2017, 35 (11) :1069-+

[7] STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): An extension of the STROBE statement [J].

Gallo, Valentina ;

Egger, Matthias ;

McCormack, Valerie ;

Farmer, Peter B. ;

Ioannidis, John P. A. ;

Kirsch-Volders, Micheline ;

Matullo, Giuseppe ;

Phillips, David H. ;

Schoket, Bernadette ;

Stromberg, Ulf ;

Vermeulen, Roel ;

Wild, Christopher ;

Porta, Miquel ;

Vineis, Paolo .

EUROPEAN JOURNAL OF CLINICAL INVESTIGATION, 2012, 42 (01) :1-16

[8] Adjusting for age improves identification of gut microbiome alterations in multiple diseases [J].

Ghosh, Tarini S. ;

Das, Mrinmoy ;

Jeffery, Ian B. ;

O'Toole, Paul W. .

ELIFE, 2020, 9

[9] Microbiome Datasets Are Compositional: And This Is Not Optional [J].

Gloor, Gregory B. ;

Macklaim, Jean M. ;

Pawlowsky-Glahn, Vera ;

Egozcue, Juan J. .

FRONTIERS IN MICROBIOLOGY, 2017, 8

[10]

Hernan M. A., 2020, CAUSAL INFERENCE WHA

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