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

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Author and article information

Journal

Journal ID (iso-abbrev): Nat Biotechnol

Title: Nature biotechnology

Publisher: Springer Science and Business Media LLC

ISSN (Electronic): 1546-1696

ISSN (Print): 1087-0156

Publication date (Electronic): August 2019

Volume: 37

Issue: 8

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.

Article

Publisher Item ID: 10.1038/s41587-019-0209-9 Mid ID: NIHMS1064803

DOI: 10.1038/s41587-019-0209-9

PMC ID: 7015180

PubMed ID: 31341288

SO-VID: 4d444ec3-8ebb-48df-939b-3dbfe27af333

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