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

Author:

Bolyen Evan1,Rideout Jai Ram1ORCID,Dillon Matthew R1,Bokulich Nicholas A1ORCID,Abnet Christian2,Al-Ghalith Gabriel A3,Alexander Harriet45,Alm Eric J67,Arumugam Manimozhiyan8ORCID,Asnicar Francesco9ORCID,Bai Yang101112,Bisanz Jordan E13,Bittinger Kyle1415,Brejnrod Asker16,Brislawn Colin J17ORCID,Brown C Titus5,Callahan Benjamin J1819,Caraballo-Rodríguez Andrés Mauricio20ORCID,Chase John1,Cope Emily121,Da Silva Ricardo20,Dorrestein Pieter C20,Douglas Gavin M22,Durall Daniel M23,Duvallet Claire6ORCID,Edwardson Christian F24ORCID,Ernst Madeleine20,Estaki Mehrbod25,Fouquier Jennifer2627,Gauglitz Julia M20ORCID,Gibson Deanna L2829,Gonzalez Antonio30,Gorlick Kestrel1,Guo Jiarong31,Hillmann Benjamin32,Holmes Susan33ORCID,Holste Hannes3034ORCID,Huttenhower Curtis3536,Huttley Gavin37,Janssen Stefan38ORCID,Jarmusch Alan K20,Jiang Lingjing39,Kaehler Benjamin37,Kang Kyo Bin2040ORCID,Keefe Christopher R1,Keim Paul1,Kelley Scott T41,Knights Dan3242,Koester Irina2043,Kosciolek Tomasz30ORCID,Kreps Jorden1,Langille Morgan GI44,Lee Joslynn45,Ley Ruth4647,Liu Yong-Xin1011ORCID,Loftfield Erikka2,Lozupone Catherine48,Maher Massoud49,Marotz Clarisse30,Martin Bryan D50ORCID,McDonald Daniel30,McIver Lauren J3536,Melnik Alexey V20,Metcalf Jessica L51,Morgan Sydney C52ORCID,Morton Jamie3049,Naimey Ahmad Turan1,Navas-Molina Jose A304953ORCID,Nothias Louis Felix20,Orchanian Stephanie B54ORCID,Pearson Talima1ORCID,Peoples Samuel L5556,Petras Daniel20ORCID,Preuss Mary Lai57,Pruesse Elmar48,Rasmussen Lasse Buur16,Rivers Adam58ORCID,Robeson, II Michael S59ORCID,Rosenthal Patrick57,Segata Nicola9ORCID,Shaffer Michael4860ORCID,Shiffer Arron1,Sinha Rashmi2,Song Se Jin30ORCID,Spear John R61ORCID,Swafford Austin D54,Thompson Luke R6263,Torres Pedro J64ORCID,Trinh Pauline65,Tripathi Anupriya203066,Turnbaugh Peter J67ORCID,Ul-Hasan Sabah68,van der Hooft Justin JJ69ORCID,Vargas Fernando66,Vázquez-Baeza Yoshiki30ORCID,Vogtmann Emily2ORCID,von Hippel Max70,Walters William46,Wan Yunhu2,Wang Mingxun20,Warren Jonathan71,Weber Kyle C5872,Williamson Chase HD1,Willis Amy D73,Xu Zhenjiang Zech30,Zaneveld Jesse R74,Zhang Yilong75,Knight Rob305476,Caporaso J Gregory121ORCID

Affiliation:

1. 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, Minnesota, USA

4. Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA

5. Department of Population Health and Reproduction, University of California, 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. University of Copenhagen, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, 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, 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. Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark

17. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA

18. Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA

19. Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA

20. Collaborative mass spectrometry innovation center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA

21. Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 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 Biology, University of British Columbia Okanagan, Okanagan, BC, Canada

26. Computational Bioscience Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA

27. Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA

28. Irving K. Barber School of Arts and Sciences, Department of Biology, The University of British Columbia, Kelowna, BC, Canada

29. Department of Medicine, The University of British Columbia, Kelowna, BC, Canada

30. Department of Pediatrics, University of California San Diego, La Jolla, CA, USA

31. Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA

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

33. Stanford University, Statistics Department, Palo Alto, CA, USA

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

35. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA

36. Broad Institute of MIT and Harvard, Cambridge, MA, USA

37. Research School of Biology, The Australian National University, Canberra, ACT, Australia

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

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

40. College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea

41. San Diego State University, Department of Biology, San Diego, CA, USA

42. Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA

43. Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA

44. Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada

45. Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA

46. Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany

47. Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA

48. Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurona, CO, USA

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

50. Department of Statistics, University of Washington, Seattle, WA, USA

51. Department of Animal Science, Colorado State University, Fort Collins, CO, USA

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

53. Mountain View, Google LLC, Mountain View, CA, USA

54. Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA

55. School of Information Studies, Syracuse University, Syracuse, NY, USA

56. School of STEM, University of Washington Bothell, Bothell, WA, USA

57. Department of Biological Sciences, Webster University, St Louis, MO, USA

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

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

60. Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurona, CO, USA

61. Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA

62. Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA

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

64. Department of Biology, San Diego State University, San Diego, 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. Department of Biostatistics, University of Washington, Seattle, WA, USA

74. University of Washington Bothell, School of STEM, Division of Biological Sciences, Bothell, WA, USA

75. Merck & Co. Inc., Kenilworth, NJ, USA

76. Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA

Abstract

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.

Publisher

PeerJ

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