Computational Biology/methods; Dysbiosis/microbiology; Humans; Microbiota/physiology; Observational Studies as Topic/methods; Translational Science, Biomedical; Research Design; Computational Biology; Dysbiosis; Microbiota; Observational Studies as Topic; Biochemistry, Genetics and Molecular Biology (all); General Biochemistry, Genetics and Molecular Biology; General Medicine
Abstract :
[en] 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.
Disciplines :
Microbiology
Author, co-author :
Mirzayi, Chloe; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA
Renson, Audrey; University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Genomic Standards Consortium
Massive Analysis and Quality Control Society
Zohra, Fatima; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA
Elsafoury, Shaimaa; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA
Geistlinger, Ludwig; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA
Kasselman, Lora J; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA
Eckenrode, Kelly; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA
van de Wijgert, Janneke; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
Loughman, Amy; Food & Mood Centre, The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria, Australia
Marques, Francine Z ; Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Victoria, Australia
MacIntyre, David A; Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
Arumugam, Manimozhiyan; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
Azhar, Rimsha; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA
Beghini, Francesco; Department CIBIO, University of Trento, Trento, Italy
Bergstrom, Kirk; Department of Biology, University of British Columbia-Okanagan Campus, Kelowna, British Columbia, Canada
Bhatt, Ami; Division of Hematology and Division of Bone Marrow Transplantation, Department of Medicine, and Department of Genetics, Stanford University, Stanford, CA, USA
Bisanz, Jordan E; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
Braun, Jonathan; Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
Bravo, Hector Corrada; Genentech, South San Francisco, CA, USA
Buck, Gregory A ; Center for Microbiome Engineering and Data Analysis, Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
Bushman, Frederic; University of Pennsylvania, Philadelphia, PA, USA
Casero, David; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
Clarke, Gerard; Department of Psychiatry and Neurobehavioural Science, and APC Microbiome Ireland, University College Cork, Cork, Ireland
Collado, Maria Carmen; Institute of Agrochemistry and Food Technology-National Research Council, Valencia, Spain
Cotter, Paul D; Teagasc Food Research Centre-Moorepark, Cork, Ireland ; APC Microbiome Ireland, University College Cork, Cork, Ireland ; VistaMilk, Cork, Ireland
Cryan, John F; APC Microbiome Ireland, University College Cork, Cork, Ireland ; Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
Demmer, Ryan T; School of Public Health, University of Minnesota, Minneapolis, MN, USA
Devkota, Suzanne; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
Elinav, Eran; Immunology Department, Weizmann Institute of Science, Rehovot, Israel ; Microbiome and Cancer Division, Deutsches Krebsforschungszentrum, Heidelberg, Germany
Escobar, Juan S; Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
Fettweis, Jennifer; Center for Microbiome Engineering and Data Analysis, Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
Finn, Robert D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
Fodor, Anthony A; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
Forslund, Sofia; Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité University Hospital, Berlin, Germany
Franke, Andre; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
Furlanello, Cesare; HK3 Lab, Rovereto, Italy
Gilbert, Jack; Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
Grice, Elizabeth; Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
Haibe-Kains, Benjamin; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
Handley, Scott; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
Herd, Pamela; McCourt School of Public Policy, Georgetown University, Washington, DC, USA
Holmes, Susan; Department of Statistics, Stanford University, Stanford, CA, USA
Jacobs, Jonathan P; Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
Karstens, Lisa; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
Knight, Rob; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
Knights, Dan; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA ; Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
Koren, Omry; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
Kwon, Douglas S; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
Langille, Morgan; Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
Lindsay, Brianna; University of Maryland School of Medicine, Institute of Human Virology, Baltimore, MD, USA
McGovern, Dermot; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
McHardy, Alice C; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany
McWeeney, Shannon; OHSU Knight Cancer Institute, Portland, OR, USA
Mueller, Noel T; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
Nezi, Luigi; Department of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico-Istituto Europeo di Oncologia, Milan, Italy
Olm, Matthew; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
Palm, Noah; Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
Pasolli, Edoardo; Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
Raes, Jeroen; Department of Microbiology and Immunology, Rega institute, KU Leuven and VIB Center for Microbiology, Leuven, Belgium
Redinbo, Matthew R; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Rühlemann, Malte; Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
Balfour Sartor, R; 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
Schloss, Patrick D; Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA
Schriml, Lynn; University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
Segal, Eran; Department of Computer Science, Weizmann Institute of Science, Rehovot, Israel
Shardell, Michelle; University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
Sharpton, Thomas; Department of Microbiology and Department of Statistics, Oregon State University, Corvallis, OR, USA
Smirnova, Ekaterina; Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
Sokol, Harry; Gastroenterology Department, Centre de Recherche Saint-Antoine, INSERM, Assistance Publique-Hôpitaux de Paris, Saint Antoine Hospital, Sorbonne Université, Paris, France
Sonnenburg, Justin L; Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
Srinivasan, Sujatha; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Thingholm, Louise B; Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
Turnbaugh, Peter J; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
Upadhyay, Vaibhav; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
Walls, Ramona L; Critical Path Institute, Tucson, AZ, USA
WILMES, Paul ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Yamada, Takuji ; Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
Zeller, Georg; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Zhang, Mingyu; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
Zhao, Ni; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
Zhao, Liping; Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
Bao, Wenjun; JMP Life Sciences, SAS Institute, Cary, NC, USA
Culhane, Aedin; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
Devanarayan, Viswanath; Eisai, Woodcliff Lake, NJ, USA
Fan, Xiaohui; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
Fischer, Matthias; Experimental Pediatric Oncology, University Children's Hospital, Cologne, Germany ; Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
Jones, Wendell; Q2 Solutions-EA Genomics, Durham, NC, USA
Kusko, Rebecca; Immuneering, Cambridge, MA, USA
Mason, Christopher E; Weill Cornell Medicine, New York, NY, USA
Mercer, Tim R; Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
Sansone, Susanna-Assunta; Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK
Scherer, Andreas; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
Shi, Leming; State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
Thakkar, Shraddha; Office of Computational Science, Office of Translational Sciences, Center for Drug Evaluation and Research, Washington, DC, USA
Tong, Weida; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food & Drug Administration, Jefferson, AR, USA
Wolfinger, Russ; Scientific Discovery and Genomics, SAS Institute, Cary, NC, USA
Hunter, Christopher; GigaScience Database, BGI Hong Kong, Hong Kong, China
Segata, Nicola ; 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
Huttenhower, Curtis ; Harvard T. H. Chan School of Public Health, Boston, MA, USA
Dowd, Jennifer B; Department of Sociology, Leverhulme Centre for Demographic Science, University of Oxford, Oxford, UK
Jones, Heidi E ; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA
Waldron, Levi ; CUNY Graduate School of Public Health and Health Policy, Institute for Implementation Science in Public Health, New York, NY, USA. levi.waldron@sph.cuny.edu
U.S. Department of Health & Human Services | NIH | National Cancer Institute Leverhulme Trust MEXT | JST | Accelerated Innovation Research Initiative Turning Top Science and Ideas into High-Impact Values
Funding text :
Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award number 5R01CA230551. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Additionally, J.B.D. was supported by the Leverhulme Trust.
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