Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Affiliations

• ¹ Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
• ² Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA.
• ³ Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
• ⁴ Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
• ⁵ Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA.
• ⁶ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
• ⁷ Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
• ⁸ Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
• ⁹ Centre for Integrative Biology, University of Trento, Trento, Italy.
• ¹⁰ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
• ¹¹ Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China.
• ¹² University of Chinese Academy of Sciences, Beijing, China.
• ¹³ Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
• ¹⁴ Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
• ¹⁵ Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
• ¹⁶ Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
• ¹⁷ Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.
• ¹⁸ Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
• ¹⁹ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
• ²⁰ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
• ²¹ Institute for Systems Biology, Seattle, WA, USA.
• ²² Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.
• ²³ Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada.
• ²⁴ A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA.
• ²⁵ Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.
• ²⁶ Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada.
• ²⁷ Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
• ²⁸ Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
• ²⁹ eScience Institute, University of Washington, Seattle, WA, USA.
• ³⁰ Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.
• ³¹ Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada.
• ³² Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
• ³³ Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
• ³⁴ Statistics Department, Stanford University, Palo Alto, CA, USA.
• ³⁵ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
• ³⁶ Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
• ³⁷ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
• ³⁸ Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.
• ³⁹ Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany.
• ⁴⁰ Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA.
• ⁴¹ School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia.
• ⁴² College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea.
• ⁴³ Department of Biology, San Diego State University, San Diego, CA, USA.
• ⁴⁴ Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA.
• ⁴⁵ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
• ⁴⁶ Department of Pediatrics, University of California San Diego, La Jolla, California, USA.
• ⁴⁷ Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.
• ⁴⁸ Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA.
• ⁴⁹ Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
• ⁵⁰ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
• ⁵¹ Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.
• ⁵² Department of Statistics, University of Washington, Seattle, WA, USA.
• ⁵³ Department of Animal Science, Colorado State University, Fort Collins, CO, USA.
• ⁵⁴ Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada.
• ⁵⁵ Google LLC, Mountain View, CA, USA.
• ⁵⁶ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
• ⁵⁷ School of Information Studies, Syracuse University, Syracuse, NY, USA.
• ⁵⁸ School of STEM, University of Washington Bothell, Bothell, WA, USA.
• ⁵⁹ Department of Biological Sciences, Webster University, St. Louis, MO, USA.
• ⁶⁰ Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.
• ⁶¹ College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
• ⁶² Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA.
• ⁶³ Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.
• ⁶⁴ Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
• ⁶⁵ Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA.
• ⁶⁶ Division of Biological Sciences, University of California San Diego, San Diego, CA, USA.
• ⁶⁷ Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
• ⁶⁸ Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA.
• ⁶⁹ Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
• ⁷⁰ Department of Mathematics, University of Arizona, Tucson, AZ, USA.
• ⁷¹ National Laboratory Service, Environment Agency, Starcross, UK.
• ⁷² College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA.
• ⁷³ Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
• ⁷⁴ Department of Biostatistics, University of Washington, Seattle, WA, USA.
• ⁷⁵ School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA.
• ⁷⁶ Merck & Co. Inc., Kenilworth, NJ, USA.
• ⁷⁷ Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu.
• ⁷⁸ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu.