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

Nature Biotechnology - Tập 37 Số 8 - Trang 852-857 - 2019
Evan Bolyen1, Jai Ram Rideout1, Matthew R. Dillon1, Nicholas A. Bokulich1, Christian C. Abnet2, Gabriel A. Al‐Ghalith3, Harriet Alexander4, Eric J. Alm5, Manimozhiyan Arumugam6, Francesco Asnicar7, Yang Bai8, Jordan E. Bisanz9, Kyle Bittinger10, Asker Brejnrod6, Colin Brislawn11, C. Titus Brown12, Benjamin J. Callahan13, Andrés Mauricio Caraballo‐Rodríguez14, John Chase1, Emily K. Cope1, Ricardo Silva14, Christian Diener15, Pieter C. Dorrestein14, Gavin Douglas16, Daniel M. Durall17, Claire Duvallet5, Christian F. Edwardson18, Madeleine Ernst14, Mehrbod Estaki19, Jennifer Fouquier20, Julia M. Gauglitz14, Sean M. Gibbons15, Deanna L. Gibson21, Antonio González22, Kestrel Gorlick1, Jiarong Guo23, Benjamin Hillmann3, Susan Holmes24, Hannes Holste22, Curtis Huttenhower25, Gavin Huttley26, Stefan Janssen27, Alan K. Jarmusch14, Lingjing Jiang28, Benjamin Kaehler26, Kyo Bin Kang14, Christopher R. Keefe1, Paul Keim1, Scott T. Kelley29, Dan Knights3, Irina Koester14, Tomasz Kościółek30, Jorden Kreps1, Morgan G. I. Langille31, Joslynn S. Lee32, Ruth E. Ley33, Yongxin Liu34, Erikka Loftfield2, Catherine Lozupone35, Massoud Maher36, Clarisse Marotz22, Bryan D Martin37, Daniel McDonald22, Lauren J. McIver25, Alexey V. Melnik14, Jessica L. Metcalf38, Sydney Morgan39, Jamie Morton22, Ahmad Turan Naimey1, José A. Navas-Molina22, Louis‐Félix Nothias14, Stephanie B. Orchanian40, Talima Pearson1, Samuel L Peoples41, Daniel Petras14, Mary L. Preuss42, Elmar Pruesse35, Lasse Buur Rasmussen6, Adam R. Rivers43, Michael S. Robeson44, Patrick Rosenthal42, Nicola Segata7, Michael Shaffer35, Arron Shiffer1, Rashmi Sinha2, Se Jin Song22, John R. Spear45, Austin D. Swafford40, Luke Thompson46, Pedro J. Torres29, Pauline Trinh47, Anupriya Tripathi22, Peter J. Turnbaugh9, Sabah Ul-Hasan48, Justin J. J. van der Hooft49, Fernando Vargas50, Yoshiki Vázquez‐Baeza22, Emily Vogtmann2, Max von Hippel51, William A. Walters33, Yunhu Wan2, Mingxun Wang14, Jonathan Warren52, Kyle C. Weber43, Charles H. D. Williamson53, Amy D. Willis54, Zhenjiang Zech Xu22, Jesse Zaneveld55, Yilong Zhang56, Qiyun Zhu22, Rob Knight40, J. Gregory Caporaso57
1Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
2Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
3Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
4Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
5Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
6Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
7Centre for Integrative Biology, University of Trento, Trento, Italy
8State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
9Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
10Division of Gastroenterology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
11Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
12Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA
13Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA
14Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
15Institute for Systems Biology, Seattle, WA, USA
16Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.
17Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
18A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
19Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada
20Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
21Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
22Department of Pediatrics; University of California San Diego; La Jolla, CA USA.
23Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
24Statistics Department, Stanford University, Palo Alto, CA, USA
25Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
26Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
27Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
28Department of Family Medicine and Public Health University of California San Diego La Jolla CA USA.
29Department of Biology, San Diego State University, San Diego, CA, USA
30Department of Pediatrics, University of California San Diego, La Jolla, California, USA
31Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
32Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
33Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
34Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China
35Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
36Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
37Department of Statistics, University of Washington, Seattle, WA, USA
38Department of Animal Science, Colorado State University, Fort Collins, CO, USA
39Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada
40Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
41School of Information Studies, Syracuse University, Syracuse, NY, USA
42Department of Biological Sciences, Webster University, St. Louis, MO, USA
43Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
44College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
45Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
46Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA
47Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
48Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, USA
49Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
50Division of Biological Sciences, University of California, San Diego, San Diego, CA, USA
51Department of Mathematics, University of Arizona, Tucson, AZ, USA
52National Laboratory Service, Environment Agency, Starcross, UK
53Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
54Department of Biostatistics, University of Washington, Seattle, WA USA
55School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA
56Merck & Co. Inc., Kenilworth, NJ, USA
57Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Smith, M. I. et al. Science 339, 548–554 (2013).

Gopalakrishnan, V. et al. Science 359, 97–103 (2018).

Gehring, C. A., Sthultz, C. M., Flores-Rentería, L., Whipple, A. V. & Whitham, T. G. Proc. Natl Acad. Sci. USA 114, 11169–11174 (2017).

Lee, K., Pletcher, S. D., Lynch, S. V., Goldberg, A. N. & Cope, E. K. Front. Cell. Infect. Microbiol. 8, 168 (2018).

Metcalf, J. L. et al. Science 351, 158–162 (2016).

Rubin, R. L. et al. Ecol. Appl. 28, 1594–1605 (2018).

Pineda, A., Kaplan, I. & Bezemer, T. M. Trends Plant Sci. 22, 770–778 (2017).

Kapono, C. A. et al. Sci. Rep. 8, 3669 (2018).

Verberkmoes, N. C. et al. ISME J. 3, 179–189 (2009).

Barr, T. et al. Gut Microbes 9, 338–356 (2018).

Callahan, B. J. et al. Nat. Methods 13, 581–3 (2016).

Amir, A. et al. mSystems 2, e00191–16 (2017).

Bokulich, N. A. et al. Microbiome 6, 90 (2018).

Janssen, S. et al. mSystems 3, e00021–18 (2018).

Bokulich, N. A. et al. mSystems 3, e00219–18 (2018).

Bokulich, N. et al. J. Open Source Softw. 3, 934 (2018).

Sedio, B. E., Rojas Echeverri, J. C., Boya, P. C. A. & Wright, S. J. Ecology 98, 616–623 (2017).

Wang, M. et al. Nat. Biotechnol. 34, 828–837 (2016).

Hillmann, B. et al. mSystems 3, e00069–18 (2018).

Truong, D. T. et al. Nat. Methods 12, 902–903 (2015).

Langille, M. G. I. et al. Nat. Biotechnol. 31, 814–821 (2013).

Kluyver, T. et al. Positioning and power in academic publishing: players, agents and agendas. in Proc. 20th International Conference on Electronic Publishing (eds Loizides, F. & Schmidt, B.) 87–90 (IOS Press, 2016).

Amstutz, P. et al. https://doi.org/10.6084/m9.figshare.3115156.v2 (2016).

Gonzalez, A. et al. Nat. Methods 15, 796–798 (2018).

Schloss, P. D. et al. Appl. Environ. Microbiol. 75, 7537–7541 (2009).

McMurdie, P. J. & Holmes, S. PLoS One 8, e61217 (2013).

Huber, W. et al. Nat. Methods 12, 115–121 (2015).

Franzosa, E. A. et al. Nat. Methods 15, 962–968 (2018).

McDonald, D. et al. Gigascience 1, 7 (2012).