Reporting guidelines for human microbiome research: the STORMS checklist.

Chloe Mirzayi, Audrey Renson, Fatima Zohra, Shaimaa Elsafoury, Ludwig Geistlinger, Lora J Kasselman, Kelly Eckenrode, Janneke van de Wijgert, Amy Loughman, Francine Z Marques, David A MacIntyre, Manimozhiyan Arumugam, Rimsha Azhar, Francesco Beghini, Kirk Bergstrom, Ami Bhatt, Jordan E Bisanz, Jonathan Braun, Hector Corrada Bravo, Gregory A Buck, Frederic Bushman, David Casero, Gerard Clarke, Maria Carmen Collado, Paul D Cotter, John F Cryan, Ryan T Demmer, Suzanne Devkota, Eran Elinav, Juan S Escobar, Jennifer Fettweis, Robert D Finn, Anthony A Fodor, Sofia Forslund, Andre Franke, Cesare Furlanello, Jack Gilbert, Elizabeth Grice, Benjamin Haibe-Kains, Scott Handley, Pamela Herd, Susan Holmes, Jonathan P Jacobs, Lisa Karstens, Rob Knight, Dan Knights, Omry Koren, Douglas S Kwon, Morgan Langille, Brianna Lindsay, Dermot McGovern, Alice C McHardy, Shannon McWeeney, Noel T Mueller, Luigi Nezi, Matthew Olm, Noah Palm, Edoardo Pasolli, Jeroen Raes, Matthew R Redinbo, Malte Rühlemann, R Balfour Sartor, Patrick D Schloss, Lynn Schriml, Eran Segal, Michelle Shardell, Thomas Sharpton, Ekaterina Smirnova, Harry Sokol, Justin L Sonnenburg, Sujatha Srinivasan, Louise B Thingholm, Peter J Turnbaugh, Vaibhav Upadhyay, Ramona L Walls, Paul Wilmes, Takuji Yamada, Georg Zeller, Mingyu Zhang, Ni Zhao, Liping Zhao, Wenjun Bao, Aedin Culhane, Viswanath Devanarayan, Joaquin Dopazo, Xiaohui Fan, Matthias Fischer, Wendell Jones, Rebecca Kusko, Christopher E Mason, Tim R Mercer, Susanna-Assunta Sansone, Andreas Scherer, Leming Shi, Shraddha Thakkar, Weida Tong, Russ Wolfinger, Christopher Hunter, Nicola Segata, Curtis Huttenhower, Jennifer B Dowd, Heidi E Jones, Levi Waldron

Journal: Nature medicine 2021;27(11):1885-1892

PMID: 34789871

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.

© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

Address: CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA.; University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.; Food & Mood Centre, The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria, Australia.; Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Victoria, Australia.; Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.; Department CIBIO, University of Trento, Trento, Italy.; Department of Biology, University of British Columbia-Okanagan Campus, Kelowna, British Columbia, Canada.; Division of Hematology and Division of Bone Marrow Transplantation, Department of Medicine, and Department of Genetics, Stanford University, Stanford, CA, USA.; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.; Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.; Genentech, South San Francisco, CA, USA.; Center for Microbiome Engineering and Data Analysis, Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.; University of Pennsylvania, Philadelphia, PA, USA.; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.; Department of Psychiatry and Neurobehavioural Science, and APC Microbiome Ireland, University College Cork, Cork, Ireland.; Institute of Agrochemistry and Food Technology-National Research Council, Valencia, Spain.; Teagasc Food Research Centre-Moorepark, Cork, Ireland.; APC Microbiome Ireland, University College Cork, Cork, Ireland.; VistaMilk, Cork, Ireland.; APC Microbiome Ireland, University College Cork, Cork, Ireland.; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.; School of Public Health, University of Minnesota, Minneapolis, MN, USA.; Immunology Department, Weizmann Institute of Science, Rehovot, Israel.; Microbiome and Cancer Division, Deutsches Krebsforschungszentrum, Heidelberg, Germany.; Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia.; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.; Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité University Hospital, Berlin, Germany.; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.; HK3 Lab, Rovereto, Italy.; Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.; Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.; McCourt School of Public Policy, Georgetown University, Washington, DC, USA.; Department of Statistics, Stanford University, Stanford, CA, USA.; Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.; Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA.; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.; Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.; University of Maryland School of Medicine, Institute of Human Virology, Baltimore, MD, USA.; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany.; OHSU Knight Cancer Institute, Portland, OR, USA.; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.; Department of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico-Istituto Europeo di Oncologia, Milan, Italy.; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.; Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.; Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.; Department of Microbiology and Immunology, Rega institute, KU Leuven and VIB Center for Microbiology, Leuven, Belgium.; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany.; Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA.; University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.; Department of Computer Science, Weizmann Institute of Science, Rehovot, Israel.; Department of Microbiology and Department of Statistics, Oregon State University, Corvallis, OR, USA.; Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA.; Gastroenterology Department, Centre de Recherche Saint-Antoine, INSERM, Assistance Publique-Hôpitaux de Paris, Saint Antoine Hospital, Sorbonne Université, Paris, France.; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.; Critical Path Institute, Tucson, AZ, USA.; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.; Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.; Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.; Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA.; JMP Life Sciences, SAS Institute, Cary, NC, USA.; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.; Eisai, Woodcliff Lake, NJ, USA.; Clinical Bioinformatics Area, Hospital Virgen del Rocio, Sevilla, Spain.; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.; Experimental Pediatric Oncology, University Children's Hospital, Cologne, Germany.; Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany.; Q2 Solutions-EA Genomics, Durham, NC, USA.; Immuneering, Cambridge, MA, USA.; Weill Cornell Medicine, New York, NY, USA.; Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia.; Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK.; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.; State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.; Office of Computational Science, Office of Translational Sciences, Center for Drug Evaluation and Research, Washington, DC, USA.; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food & Drug Administration, Jefferson, AR, USA.; Scientific Discovery and Genomics, SAS Institute, Cary, NC, USA.; GigaScience Database, BGI Hong Kong, Hong Kong, China.; Department CIBIO, University of Trento, Trento, Italy.; Department of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico-Istituto Europeo di Oncologia, Milan, Italy.; Harvard T. H. Chan School of Public Health, Boston, MA, USA.; Department of Sociology, Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK.; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA. [email protected].
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