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