Nature Medicine

, volume 27 , issue 11 , pages 1885-1892

Reporting guidelines for human microbiome research: the STORMS checklist

Chloe Mirzayi ¹

Audrey Renson ²

Fatima Zohra ¹

Shaimaa Elsafoury ¹

Ludwig Geistlinger ¹

Lora J. Kasselman ³

Kelly Eckenrode ⁴

Janneke van de Wijgert ⁵

Amy Loughman ⁶

Francine Z. Marques ⁷

David A. MacIntyre ¹

Manimozhiyan Arumugam ⁸

Rimsha Azhar ⁹

Francesco Beghini ¹⁰

Kirk Bergstrom ¹¹

Ami Bhatt ¹²

Jordan E. Bisanz ¹³

Jonathan Braun ¹⁴

Héctor Corrada Bravo ¹⁵

Gregory A. Buck ¹⁶

Frederic Bushman ¹⁷

David Casero ¹⁸

Gerard Clarke ^{19, 20, 21}

Maria Carmen Collado ^{20, 22}

Paul D. Cotter ²³

John F. Cryan ¹⁶

Ryan T Demmer ^{24, 25}

Suzanne Devkota ²⁶

Eran Elinav ¹⁴

Juan S Escobar ²⁷

Jennifer Fettweis ²⁸

Robert D. Finn ²⁹

Anthony A. Fodor ³⁰

Sofia Forslund ³¹

Andre Franke ³²

CESARE FURLANELLO ³³

Jack Gilbert ³⁴

Elizabeth Grice ³⁵

Benjamin Haibe-Kains ³⁶

Scott Handley ³⁷

Pamela Herd ³⁸

Susan Holmes ³⁹

Jonathan P. Jacobs ⁴⁰

Lisa Karstens ^{41, 42}

Rob Knight ⁴³

Dan Knights ⁴⁴

Omry Koren ⁴⁵

Douglas S. Kwon ⁴⁶

Morgan Langille ¹⁶

Brianna Lindsay ⁴⁷

Dermot McGovern ⁴⁸

Alice C McHardy ⁴⁹

Shannon McWeeney ⁵⁰

Noel T Mueller ⁵¹

Luigi Nezi ⁵²

Matthew Olm ⁵³

Noah Palm ⁵⁴

Edoardo Pasolli ⁵⁵

Jeroen Raes ⁵⁶

Matthew R. Redinbo ⁵⁷

Malte Rühlemann ⁵⁸

R. Balfour Sartor ⁵⁹

Patrick D Schloss ⁶⁰

Lynn Schriml ⁵⁹

Eran Segal ⁶¹

Michelle Shardell ⁶²

Thomas Sharpton ⁶³

Ekaterina Smirnova ⁵¹

Harry Sokol ⁶⁴

Justin L. Sonnenburg ⁵⁶

Sujatha Srinivasan ⁶⁵

Louise B Thingholm ⁶⁵

Peter J Turnbaugh ⁶⁶

Vaibhav Upadhyay ^{67, 68}

Ramona L. Walls ⁶⁹

Paul Wilmes ⁷⁰

Takuji YAMADA ⁴⁹

Georg Zeller ⁷¹

Mingyu Zhang ⁷²

Zhao Ni ⁷³

Liping Zhao ⁷⁴

Wenjun Bao ⁷⁵

Aedin Culhane ⁷⁶

Viswanath Devanarayan ⁷⁷

Joaquín Dopazo ^{78, 79}

Xiaohui Fan ⁸⁰

Matthias Fischer ⁸¹

Wendell Jones ⁸²

Rebecca Kusko ⁸³

Christopher E. Mason ⁸⁴

Tim R. Mercer ⁸⁵

Susanna-Assunta Sansone ⁸⁶

Andreas Scherer ⁸⁷

Leming Shi ⁸⁸

Shraddha Thakkar ⁸⁹

Weida Tong ⁹⁰

Russ Wolfinger ^{8, 50}

Christopher Hunter ⁹¹

Nicola Segata ⁹²

Curtis Huttenhower ¹

Jennifer B Dowd ¹

Hide authors affiliations Show authors affiliations: 92 affiliations

CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, USA |

University of North Carolina at Chapel hill, Chapel hill, USA |

Julius Center for Health Sciences and Primary care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands |

⁴

Food & Mood Centre, The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia |

⁵

Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Australia |

⁶

Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK |

⁷

Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

University of Copenhagen

Novo Nordisk

⁸

Department CIBIO, University of Trento, Trento, Italy |

⁹

Department of Biology, University of British Columbia–Okanagan Campus, Kelowna, Canada |

¹⁰

Division of Hematology and Division of Bone Marrow Transplantation, Department of Medicine, and Department of Genetics, Stanford University, Stanford, USA |

¹¹

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, USA |

¹²

Division of Gastroenterology and Hepatology, Department of Medicine, Cedars–Sinai Medical Center, Los Angeles, USA |

¹³

Genentech, South San Francisco, USA |

¹⁴

Center for Microbiome Engineering and Data Analysis, Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, USA |

¹⁵

University of Pennsylvania, Philadelphia, USA |

¹⁶

F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars–Sinai Medical Center, Los Angeles, USA |

¹⁷

Department of Psychiatry and Neurobehavioural Science, and APC Microbiome Ireland, University College Cork, Cork, Ireland |

¹⁸

Institute of Agrochemistry and Food Technology-National Research Council, Valencia, Spain |

¹⁹

Teagasc Food Research Centre–Moorepark, Cork, Ireland |

²⁰

APC microbiome Ireland, University College Cork, Cork, Ireland |

²¹

VistaMilk, Cork, Ireland |

²²

Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland |

²³

School of Public Health, University of Minnesota, Minneapolis, USA |

²⁴

Immunology department, Weizmann Institute of Science, Rehovot, Israel |

²⁵

Microbiome and Cancer Division, Deutsches Krebsforschungszentrum, Heidelberg, Germany |

²⁶

Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia |

²⁷

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK |

²⁸

Department of Bioinformatics and Genomics, University of North Carolina At Charlotte, Charlotte, USA |

²⁹

Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité University Hospital, Berlin, Germany |

³⁰

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany |

³¹

HK3 Lab, Rovereto, Italy |

³²

Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA

University of California, San Diego

Scripps Institution of Oceanography

³³

Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA |

³⁴

Princess Margaret Cancer Centre, University Health Network, toronto, Canada |

³⁵

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, USA |

³⁶

McCourt School of Public Policy, Georgetown University, Washington, USA |

³⁷

Department of Statistics, Stanford University, Stanford, USA |

³⁸

Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, USA |

³⁹

Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, USA |

⁴⁰

Center for Microbiome Innovation, University of California San Diego, La Jolla, USA |

⁴¹

Department of Computer Science and Engineering, University of Minnesota, Minneapolis, USA |

⁴²

Biotechnology Institute, University of Minnesota, Saint Paul, USA |

⁴³

Azrieli faculty of Medicine, Bar Ilan University, Safed, Israel |

⁴⁴

Division of Infectious Diseases, Massachusetts General Hospital, Boston, USA |

⁴⁵

Department of Pharmacology, Dalhousie University, Halifax, Canada |

⁴⁶

University of Maryland School of Medicine, Institute of Human Virology, Baltimore, USA |

⁴⁷

Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany |

⁴⁸

OHSU Knight Cancer Institute, Portland, USA |

⁴⁹

Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA |

⁵⁰

Department of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico–Istituto Europeo di Oncologia, Milan, Italy |

⁵¹

Department of Microbiology and Immunology, Stanford University, Stanford, USA |

⁵²

Department of Immunobiology, Yale University School of Medicine, New Haven, USA |

⁵³

Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy |

⁵⁴

Department of Microbiology and Immunology, Rega institute, KU Leuven and VIB Center for Microbiology, Leuven, Belgium |

⁵⁵

Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, USA |

⁵⁶

Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany |

⁵⁷

Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA |

⁵⁸

Department of Microbiology & Immunology, University of Michigan, Ann Arbor, USA |

⁵⁹

University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, USA |

⁶⁰

Department of Computer Science, Weizmann institute of Science, Rehovot, Israel |

⁶¹

Department of Microbiology and Department of Statistics, Oregon State University, Corvallis, USA |

⁶²

Department of Biostatistics, Virginia Commonwealth University, Richmond, USA |

⁶³

Gastroenterology Department, Centre de Recherche Saint-Antoine, INSERM, Assistance Publique–Hôpitaux de Paris, Saint Antoine Hospital, Sorbonne Université, Paris, France

Sorbonne University

French Institute of Health and Medical Research

⁶⁴

Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA |

⁶⁵

Department of Microbiology and Immunology, University of California San Francisco, San Francisco, USA |

⁶⁶

Critical PATH Institute, Tucson, USA |

⁶⁷

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg |

⁶⁸

Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-Sur-Alzette, Luxembourg |

⁶⁹

Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan |

⁷⁰

Structural and computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany |

⁷¹

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA |

⁷²

Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, USA |

⁷³

JMP Life Sciences, SAS Institute, Cary, USA |

⁷⁴

Department of Data Sciences, Dana–Farber Cancer Institute, Boston, USA |

⁷⁵

Eisai, Woodcliff Lake, USA |

⁷⁶

Clinical Bioinformatics Area, Hospital Virgen del Rocio, Sevilla, Spain |

⁷⁷

College of pharmaceutical Sciences, Zhejiang University, Hangzhou, China |

⁷⁸

Experimental Pediatric Oncology, University Children’s Hospital, Cologne, Germany |

⁷⁹

Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany |

⁸⁰

Q2 Solutions-EA Genomics, Durham, USA |

⁸¹

Immuneering, Cambridge, USA |

⁸²

Weill Cornell Medicine, New York, USA |

⁸³

Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Australia |

⁸⁴

Oxford E-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK |

⁸⁵

Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland

University of Helsinki

Institute for Molecular Medicine Finland

⁸⁶

State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China |

⁸⁷

Office of Computational Science, Office of Translational Sciences, Center for Drug Evaluation and Research, Washington, USA |

⁸⁸

Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food & Drug Administration, Jefferson, USA |

⁸⁹

Scientific Discovery and Genomics, SAS Institute, Cary, USA |

⁹⁰

GigaScience Database, BGI Hong Kong, Hong Kong, China |

⁹¹

Harvard T. H. Chan School of Public Health, Boston, USA |

⁹²

Department of Sociology, Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK |

Publication type: Journal Article

Publication date: 2021-11-17

Springer Nature

Nature Medicine

scimago Q1

wos Q1

SJR: 18.333

CiteScore: 82.4

Impact factor: 50.0

ISSN: 10788956, 1546170X, 17447933

DOI: 10.1038/s41591-021-01552-x

Copy DOI

PubMed ID: 34789871

General Biochemistry, Genetics and Molecular Biology

General Medicine

Abstract

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.

Found

1 citation

Karolina Ana

3 publications, 55 citations

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Mirzayi C. et al. Reporting guidelines for human microbiome research: the STORMS checklist // Nature Medicine. 2021. Vol. 27. No. 11. pp. 1885-1892.

GOST all authors (up to 50) Copy

Mirzayi C. et al. Reporting guidelines for human microbiome research: the STORMS checklist // Nature Medicine. 2021. Vol. 27. No. 11. pp. 1885-1892.

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BibTex (up to 50 authors) Copy

@article{2021_Mirzayi,

author = {Chloe Mirzayi and Audrey Renson and Fatima Zohra and Shaimaa Elsafoury and Ludwig Geistlinger and Lora J. Kasselman and Kelly Eckenrode and Janneke van de Wijgert and Amy Loughman and Francine Z. Marques and David A. MacIntyre and Manimozhiyan Arumugam and Rimsha Azhar and Francesco Beghini and Kirk Bergstrom and Ami Bhatt and Jordan E. Bisanz and Jonathan Braun and Héctor Corrada Bravo and Gregory A. Buck and Frederic Bushman and David Casero and Gerard Clarke and Maria Carmen Collado and Paul D. Cotter and John F. Cryan and Ryan T Demmer and Suzanne Devkota and Eran Elinav and Juan S Escobar and Jennifer Fettweis and Robert D. Finn and Anthony A. Fodor and Sofia Forslund and Andre Franke and CESARE FURLANELLO and Jack Gilbert and Elizabeth Grice and Benjamin Haibe-Kains and Scott Handley and Pamela Herd and Susan Holmes and Jonathan P. Jacobs and Lisa Karstens and Rob Knight and Dan Knights and Omry Koren and Douglas S. Kwon and Morgan Langille and Brianna Lindsay and others},

title = {Reporting guidelines for human microbiome research: the STORMS checklist},

journal = {Nature Medicine},

year = {2021},

volume = {27},

publisher = {Springer Nature},

month = {nov},

url = {https://doi.org/10.1038/s41591-021-01552-x},

number = {11},

pages = {1885--1892},

doi = {10.1038/s41591-021-01552-x}

}

MLA

Cite this

MLA Copy

Mirzayi, Chloe, et al. “Reporting guidelines for human microbiome research: the STORMS checklist.” Nature Medicine, vol. 27, no. 11, Nov. 2021, pp. 1885-1892. https://doi.org/10.1038/s41591-021-01552-x.

Publisher

Springer Nature

Journal

Nature Medicine

scimago Q1

wos Q1

SJR

18.333

CiteScore

82.4

Impact factor

50.0

ISSN

10788956 (Print)

1546170X (Electronic)

17447933 (Electronic)