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

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Journal

Journal ID (nlm-journal-id): 9604648

Journal ID (pubmed-jr-id): 20305

Journal ID (nlm-ta): Nat Biotechnol

Journal ID (iso-abbrev): Nat. Biotechnol.

Title: Nature biotechnology

ISSN (Print): 1087-0156

ISSN (Electronic): 1546-1696

Publication date Nihms-submitted: 25 December 2019

Publication date (Print): August 2019

Publication date PMC-release: 12 February 2020

Volume: 37

Issue: 8

Pages: 852-857

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 ]Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.

[35 ]Statistics Department, Stanford University, Palo Alto, CA, USA.

[36 ]Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

[37 ]Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

[38 ]Broad Institute of MIT and Harvard, Cambridge, MA, USA.

[39 ]Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.

[40 ]Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany.

[41 ]Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA.

[42 ]School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia.

[43 ]College of Pharmacy, Sookmyung Women’s University, Seoul, Republic of Korea.

[44 ]Department of Biology, San Diego State University, San Diego, CA, USA.

[45 ]Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA.

[46 ]Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.

[47 ]Department of Pediatrics, University of California San Diego, La Jolla, California, USA.

[48 ]Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.

[49 ]Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA.

[50 ]Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.

[51 ]Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.

[52 ]Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.

[53 ]Department of Statistics, University of Washington, Seattle, WA, USA.

[54 ]Department of Animal Science, Colorado State University, Fort Collins, CO, USA.

[55 ]Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada.

[56 ]Google LLC, Mountain View, CA, USA.

[57 ]Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.

[58 ]School of Information Studies, Syracuse University, Syracuse, NY, USA.

[59 ]School of STEM, University of Washington Bothell, Bothell, WA, USA.

[60 ]Department of Biological Sciences, Webster University, St. Louis, MO, USA.

[61 ]Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.

[62 ]College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.

[63 ]Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA.

[64 ]Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.

[65 ]Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.

[66 ]Department of Biology, San Diego State University, San Diego, CA, USA.

[67 ]Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA.

[68 ]Division of Biological Sciences, University of California San Diego, San Diego, CA, USA.

[69 ]Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.

[70 ]Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA.

[71 ]Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.

[72 ]Department of Mathematics, University of Arizona, Tucson, AZ, USA.

[73 ]National Laboratory Service, Environment Agency, Starcross, UK.

[74 ]College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA.

[75 ]Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.

[76 ]Department of Biostatistics, University of Washington, Seattle, WA, USA.

[77 ]School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA.

[78 ]Merck & Co. Inc., Kenilworth, NJ, USA.

[79 ]Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

[80 ]These authors contributed equally: Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich.

Author notes

[* ] greg.caporaso@ 123456nau.edu

Author contributions

E.B., J.R.R., M.R.D., N.A.B., Y.B., J.E.B., C.J.B., A.M.C.-R., E.K.C., C. Diener, R.D., C.F.E., M. Ernst, M. Estaki, A.G., J.M.G., D.L.G., S.M.G., A.K.J., K.B.K., S.T.K., I.K., T.K., J.L., Y.-X.L., A.V.M., J.L.M., L.F.N., S.B.O., D.P., A.S., S.J.S., A.D.S., L.R.T., P. J. Torres, P. J. Turnbaugh, S.U.-H., F.V., J.W., R.K. and J.G.C. developed documentation, educational materials and/or user/developer support content. E.B., J.R.R., M.R.D., N.A.B., R.K. and J.G.C. wrote the manuscript; all authors assisted with revision of the manuscript. E.B., J.R.R., M.R.D., N.A.B. and J.G.C. designed and developed the QIIME 2 framework. D.M.D., A.G., R.L., E.L., S.C.M., R.S., J.R.S., W.W., C.H.D.W. and R.K. contributed data used in the manuscript and/or testing of QIIME 2. C.C.A., C.T.B., E.K.C., P.C.D., S.H., P.K., E.L., T.P., R.S., E.V., Y.W. and R.K. contributed to the design of analytical methods. E.B., J.R.R., M.R.D., N.A.B., G.A.A.-G., H.A., E.J.A., M.A., F.A., K.B., A.B., B.J.C., J.C., G.M.D., C. Duvallet, M. Ernst, J.F., A.G., K.G., J.G., S.M.G., B.H., H.H., C.H., G.H., S.J., L.J., B.D.K., C.R.K., D.K., J.K., M.G.I.L., C.L., M.M., C.M., B.D.M., D.M., L.J.M., J.T.M., A.T.N., J.A.N.-M., S.L.P., M.L.P., E.P., L.B.R., A.R., M.S.R., P.R., N.S., M.S., P.T., A.T., J.J.J.v.d.H., Y.V.-B., M.V., M.W., K.C.W., A.D.W., Z.Z.X., J.R.Z., Y.Z., Q.Z. and J.G.C. contributed software to QIIME 2 plugins, interfaces, framework and/or build and test systems.

Author information

Evan Bolyen http://orcid.org/0000-0002-5362-6782

Jai Ram Rideout http://orcid.org/0000-0003-2587-1454

Matthew R. Dillon http://orcid.org/0000-0002-7713-1952

Nicholas A. Bokulich http://orcid.org/0000-0002-1784-8935

Christian C. Abnet http://orcid.org/0000-0002-3008-7843

Gabriel A. Al-Ghalith http://orcid.org/0000-0002-6953-6319

Eric J. Alm http://orcid.org/0000-0001-8294-9364

Manimozhiyan Arumugam http://orcid.org/0000-0002-0886-9101

Francesco Asnicar http://orcid.org/0000-0003-3732-1468

Yang Bai http://orcid.org/0000-0003-2652-7022

Jordan E. Bisanz http://orcid.org/0000-0002-8649-1706

C. Titus Brown http://orcid.org/0000-0001-6001-2677

Benjamin J. Callahan http://orcid.org/0000-0002-8752-117X

Andrés Mauricio Caraballo-Rodríguez http://orcid.org/0000-0001-5499-2728

Christian Diener http://orcid.org/0000-0002-7476-0868

Pieter C. Dorrestein http://orcid.org/0000-0002-3003-1030

Daniel M. Durall http://orcid.org/0000-0001-7414-4443

Claire Duvallet http://orcid.org/0000-0002-8093-8394

Christian F. Edwardson http://orcid.org/0000-0001-7524-7209

Jennifer Fouquier http://orcid.org/0000-0002-0975-8235

Sean M. Gibbons http://orcid.org/0000-0002-8724-7916

Susan Holmes http://orcid.org/0000-0002-2208-8168

Hannes Holste http://orcid.org/0000-0001-7739-6590

Curtis Huttenhower http://orcid.org/0000-0002-1110-0096

Stefan Janssen http://orcid.org/0000-0003-0955-0589

Kyo Bin Kang http://orcid.org/0000-0003-3290-1017

Christopher R. Keefe http://orcid.org/0000-0002-4289-0991

Tomasz Kosciolek http://orcid.org/0000-0002-9915-7387

Jorden Kreps http://orcid.org/0000-0003-3758-6458

Yong-Xin Liu http://orcid.org/0000-0003-1832-9835

Erikka Loftfield http://orcid.org/0000-0002-3573-8748

Catherine Lozupone http://orcid.org/0000-0003-4786-7202

Clarisse Marotz http://orcid.org/0000-0002-1520-8854

Bryan D. Martin http://orcid.org/0000-0002-8002-5296

Daniel McDonald http://orcid.org/0000-0003-0876-9060

Alexey V. Melnik http://orcid.org/0000-0002-4645-8880

Jose A. Navas-Molina http://orcid.org/0000-0003-4595-920X

Stephanie B. Orchanian http://orcid.org/0000-0002-2491-1074

Talima Pearson http://orcid.org/0000-0003-3696-041X

Daniel Petras http://orcid.org/0000-0002-6561-3022

Adam Rivers http://orcid.org/0000-0002-3703-834X

Michael S. Robeson II http://orcid.org/0000-0001-7119-6301

Nicola Segata http://orcid.org/0000-0002-1583-5794

Se Jin Song http://orcid.org/0000-0003-0750-5709

Luke R. Thompson http://orcid.org/0000-0002-3911-1280

Peter J. Turnbaugh http://orcid.org/0000-0002-0888-2875

Justin J. J. vander Hooft http://orcid.org/0000-0002-9340-5511

Emily Vogtmann http://orcid.org/0000-0003-1355-5593

Max von Hippel http://orcid.org/0000-0003-0288-5802

Jonathan Warren http://orcid.org/0000-0003-3381-3852

Amy D. Willis http://orcid.org/0000-0002-2802-4317

Qiyun Zhu http://orcid.org/0000-0002-3568-6271

Rob Knight http://orcid.org/0000-0002-0975-9019

J. Gregory Caporaso http://orcid.org/0000-0002-8865-1670

Article

Accession ID: PMC7015180 Pmcid ID: PMC7015180 Pmc-uid ID: 7015180 Manuscript ID: nihpa1064803

DOI: 10.1038/s41587-019-0209-9

PMC ID: 7015180

PubMed ID: 31341288

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

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