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

Evan Bolyen; Jai Ram Rideout; Matthew R. Dillon; Nicholas A. Bokulich; Christian C. Abnet; Gabriel A. Al-Ghalith; Harriet Alexander; Eric J. Alm; Manimozhiyan Arumugam; Francesco Asnicar; Yang Bai; Jordan E. Bisanz; Kyle Bittinger; Asker Brejnrod; Colin J. Brislawn; C. Titus Brown; Benjamin J. Callahan; Andrés Mauricio Caraballo-Rodríguez; John Chase; Emily K. Cope; Ricardo Da Silva; Christian Diener; Pieter C. Dorrestein; Gavin M. Douglas; Daniel M. Durall; Claire Duvallet; Christian F. Edwardson; Madeleine Ernst; Mehrbod Estaki; Jennifer Fouquier; Julia M. Gauglitz; Sean M. Gibbons; Deanna L. Gibson; Antonio Gonzalez; Kestrel Gorlick; Jiarong Guo; Benjamin Hillmann; Susan Holmes; Hannes Holste; Curtis Huttenhower; Gavin A. Huttley; Stefan Janssen; Alan K. Jarmusch; Lingjing Jiang; Benjamin D. Kaehler; Kyo Bin Kang; Christopher R. Keefe; Paul Keim; Scott T. Kelley; Dan Knights; Irina Koester; Tomasz Kosciolek; Jorden Kreps; Morgan G.I. Langille; Joslynn Lee; Ruth Ley; Yong Xin Liu; Erikka Loftfield; Catherine Lozupone; Massoud Maher; Clarisse Marotz; Bryan D. Martin; Daniel McDonald; Lauren J. McIver; Alexey V. Melnik; Jessica L. Metcalf; Sydney C. Morgan; Jamie T. Morton; Ahmad Turan Naimey; Jose A. Navas-Molina; Louis Felix Nothias; Stephanie B. Orchanian; Talima Pearson; Samuel L. Peoples; Daniel Petras; Mary Lai Preuss; Elmar Pruesse; Lasse Buur Rasmussen; Adam Rivers; Michael S. Robeson; Patrick Rosenthal; Nicola Segata; Michael Shaffer; Arron Shiffer; Rashmi Sinha; Se Jin Song; John R. Spear; Austin D. Swafford; Luke R. Thompson; Pedro J. Torres; Pauline Trinh; Anupriya Tripathi; Peter J. Turnbaugh; Sabah Ul-Hasan; Justin J.J. van der Hooft; Fernando Vargas; Yoshiki Vázquez-Baeza; Emily Vogtmann; Max von Hippel; William Walters; Yunhu Wan; Mingxun Wang; Jonathan Warren; Kyle C. Weber; Charles H.D. Williamson; Amy D. Willis; Zhenjiang Zech Xu; Jesse R. Zaneveld; Yilong Zhang; Qiyun Zhu; Rob Knight; J. Gregory Caporaso

doi:10.1038/s41587-019-0209-9

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

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E. Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J. Brislawn, C. Titus Brown, Benjamin J. Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K. CopeRicardo Da Silva, Christian Diener, Pieter C. Dorrestein, Gavin M. Douglas, Daniel M. Durall, Claire Duvallet, Christian F. Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M. Gauglitz, Sean M. Gibbons, Deanna L. Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A. Huttley, Stefan Janssen, Alan K. Jarmusch, Lingjing Jiang, Benjamin D. Kaehler, Kyo Bin Kang, Christopher R. Keefe, Paul Keim, Scott T. Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G.I. Langille, Joslynn Lee, Ruth Ley, Yong Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D. Martin, Daniel McDonald, Lauren J. McIver, Alexey V. Melnik, Jessica L. Metcalf, Sydney C. Morgan, Jamie T. Morton, Ahmad Turan Naimey, Jose A. Navas-Molina, Louis Felix Nothias, Stephanie B. Orchanian, Talima Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R. Spear, Austin D. Swafford, Luke R. Thompson, Pedro J. Torres, Pauline Trinh, Anupriya Tripathi, Peter J. Turnbaugh, Sabah Ul-Hasan, Justin J.J. van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C. Weber, Charles H.D. Williamson, Amy D. Willis, Zhenjiang Zech Xu, Jesse R. Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J. Gregory Caporaso

Research output: Contribution to journal › Letter › peer-review

11348 Scopus citations

Original language	English (US)
Pages (from-to)	852-857
Number of pages	6
Journal	Nature Biotechnology
Volume	37
Issue number	8
DOIs	https://doi.org/10.1038/s41587-019-0209-9
State	Published - Aug 1 2019

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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10.1038/s41587-019-0209-9

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Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., ... Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852-857. https://doi.org/10.1038/s41587-019-0209-9

Bolyen, E, Rideout, JR, Dillon, MR, Bokulich, NA, Abnet, CC, Al-Ghalith, GA, Alexander, H, Alm, EJ, Arumugam, M, Asnicar, F, Bai, Y, Bisanz, JE, Bittinger, K, Brejnrod, A, Brislawn, CJ, Brown, CT, Callahan, BJ, Caraballo-Rodríguez, AM, Chase, J, Cope, EK, Da Silva, R, Diener, C, Dorrestein, PC, Douglas, GM, Durall, DM, Duvallet, C, Edwardson, CF, Ernst, M, Estaki, M, Fouquier, J, Gauglitz, JM, Gibbons, SM, Gibson, DL, Gonzalez, A, Gorlick, K, Guo, J, Hillmann, B, Holmes, S, Holste, H, Huttenhower, C, Huttley, GA, Janssen, S, Jarmusch, AK, Jiang, L, Kaehler, BD, Kang, KB, Keefe, CR, Keim, P, Kelley, ST, Knights, D, Koester, I, Kosciolek, T, Kreps, J, Langille, MGI, Lee, J, Ley, R, Liu, YX, Loftfield, E, Lozupone, C, Maher, M, Marotz, C, Martin, BD, McDonald, D, McIver, LJ, Melnik, AV, Metcalf, JL, Morgan, SC, Morton, JT, Naimey, AT, Navas-Molina, JA, Nothias, LF, Orchanian, SB, Pearson, T, Peoples, SL, Petras, D, Preuss, ML, Pruesse, E, Rasmussen, LB, Rivers, A, Robeson, MS, Rosenthal, P, Segata, N, Shaffer, M, Shiffer, A, Sinha, R, Song, SJ, Spear, JR, Swafford, AD, Thompson, LR, Torres, PJ, Trinh, P, Tripathi, A, Turnbaugh, PJ, Ul-Hasan, S, van der Hooft, JJJ, Vargas, F, Vázquez-Baeza, Y, Vogtmann, E, von Hippel, M, Walters, W, Wan, Y, Wang, M, Warren, J, Weber, KC, Williamson, CHD, Willis, AD, Xu, ZZ, Zaneveld, JR, Zhang, Y, Zhu, Q, Knight, R & Caporaso, JG 2019, 'Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2', Nature Biotechnology, vol. 37, no. 8, pp. 852-857. https://doi.org/10.1038/s41587-019-0209-9

@article{5c42177008a54c7391bd20d171fc6284,

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

author = "Evan Bolyen and Rideout, {Jai Ram} and Dillon, {Matthew R.} and Bokulich, {Nicholas A.} and Abnet, {Christian C.} and Al-Ghalith, {Gabriel A.} and Harriet Alexander and Alm, {Eric J.} and Manimozhiyan Arumugam and Francesco Asnicar and Yang Bai and Bisanz, {Jordan E.} and Kyle Bittinger and Asker Brejnrod and Brislawn, {Colin J.} and Brown, {C. Titus} and Callahan, {Benjamin J.} and Caraballo-Rodr{\'i}guez, {Andr{\'e}s Mauricio} and John Chase and Cope, {Emily K.} and {Da Silva}, Ricardo and Christian Diener and Dorrestein, {Pieter C.} and Douglas, {Gavin M.} and Durall, {Daniel M.} and Claire Duvallet and Edwardson, {Christian F.} and Madeleine Ernst and Mehrbod Estaki and Jennifer Fouquier and Gauglitz, {Julia M.} and Gibbons, {Sean M.} and Gibson, {Deanna L.} and Antonio Gonzalez and Kestrel Gorlick and Jiarong Guo and Benjamin Hillmann and Susan Holmes and Hannes Holste and Curtis Huttenhower and Huttley, {Gavin A.} and Stefan Janssen and Jarmusch, {Alan K.} and Lingjing Jiang and Kaehler, {Benjamin D.} and Kang, {Kyo Bin} and Keefe, {Christopher R.} and Paul Keim and Kelley, {Scott T.} and Dan Knights and Irina Koester and Tomasz Kosciolek and Jorden Kreps and Langille, {Morgan G.I.} and Joslynn Lee and Ruth Ley and Liu, {Yong Xin} and Erikka Loftfield and Catherine Lozupone and Massoud Maher and Clarisse Marotz and Martin, {Bryan D.} and Daniel McDonald and McIver, {Lauren J.} and Melnik, {Alexey V.} and Metcalf, {Jessica L.} and Morgan, {Sydney C.} and Morton, {Jamie T.} and Naimey, {Ahmad Turan} and Navas-Molina, {Jose A.} and Nothias, {Louis Felix} and Orchanian, {Stephanie B.} and Talima Pearson and Peoples, {Samuel L.} and Daniel Petras and Preuss, {Mary Lai} and Elmar Pruesse and Rasmussen, {Lasse Buur} and Adam Rivers and Robeson, {Michael S.} and Patrick Rosenthal and Nicola Segata and Michael Shaffer and Arron Shiffer and Rashmi Sinha and Song, {Se Jin} and Spear, {John R.} and Swafford, {Austin D.} and Thompson, {Luke R.} and Torres, {Pedro J.} and Pauline Trinh and Anupriya Tripathi and Turnbaugh, {Peter J.} and Sabah Ul-Hasan and {van der Hooft}, {Justin J.J.} and Fernando Vargas and Yoshiki V{\'a}zquez-Baeza and Emily Vogtmann and {von Hippel}, Max and William Walters and Yunhu Wan and Mingxun Wang and Jonathan Warren and Weber, {Kyle C.} and Williamson, {Charles H.D.} and Willis, {Amy D.} and Xu, {Zhenjiang Zech} and Zaneveld, {Jesse R.} and Yilong Zhang and Qiyun Zhu and Rob Knight and Caporaso, {J. Gregory}",

note = "Funding Information: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award. Thanks to the Yellowstone Center for Resources for research permit no. 5664 to J.R.S. for Yellowstone access and sample collection. We thank P. J. McMurdie for helpful discussion on the relationships between QIIME 2 and phyloseq. We would like to thank the users of QIIME 1 and 2, whose invaluable feedback has shaped QIIME 2. In particular, we would like to thank A. Abdelfattah (Stockholm University, Sweden), R. C. T. Boutin (University of British Columbia, Canada), D. J. Bradshaw II (Florida Atlantic University Harbor Branch Oceanographic Institute, USA), L. Bullington (MPG Ranch, USA), J. W. Debelius (Karolinska Institutet, Sweden), C. Duvallet (Massachusetts Institute of Technology, USA), E. Korzune Ganda (Cornell University, USA), A. Mahnert (Medical University of Graz, Austria), M. C. Melendrez (St. Cloud State University, USA), D. O{\textquoteright}Rourke (University of New Hampshire, USA), A. R. Rivers (USDA ARS, USA), B. Sen (Tianjin University, China), S. Tangedal (Haukeland University Hospital and University of Bergen, Norway), P. J. Torres (San Diego State University, USA) and J. Warren (National Laboratory Service, UK) for writing end-user reviews included in the Supplementary Methods.",

year = "2019",

month = aug,

day = "1",

doi = "10.1038/s41587-019-0209-9",

language = "English (US)",

volume = "37",

pages = "852--857",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "8",

}

TY - JOUR

T1 - Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

AU - Bolyen, Evan

AU - Rideout, Jai Ram

AU - Dillon, Matthew R.

AU - Bokulich, Nicholas A.

AU - Abnet, Christian C.

AU - Al-Ghalith, Gabriel A.

AU - Alexander, Harriet

AU - Alm, Eric J.

AU - Arumugam, Manimozhiyan

AU - Asnicar, Francesco

AU - Bai, Yang

AU - Bisanz, Jordan E.

AU - Bittinger, Kyle

AU - Brejnrod, Asker

AU - Brislawn, Colin J.

AU - Brown, C. Titus

AU - Callahan, Benjamin J.

AU - Caraballo-Rodríguez, Andrés Mauricio

AU - Chase, John

AU - Cope, Emily K.

AU - Da Silva, Ricardo

AU - Diener, Christian

AU - Dorrestein, Pieter C.

AU - Douglas, Gavin M.

AU - Durall, Daniel M.

AU - Duvallet, Claire

AU - Edwardson, Christian F.

AU - Ernst, Madeleine

AU - Estaki, Mehrbod

AU - Fouquier, Jennifer

AU - Gauglitz, Julia M.

AU - Gibbons, Sean M.

AU - Gibson, Deanna L.

AU - Gonzalez, Antonio

AU - Gorlick, Kestrel

AU - Guo, Jiarong

AU - Hillmann, Benjamin

AU - Holmes, Susan

AU - Holste, Hannes

AU - Huttenhower, Curtis

AU - Huttley, Gavin A.

AU - Janssen, Stefan

AU - Jarmusch, Alan K.

AU - Jiang, Lingjing

AU - Kaehler, Benjamin D.

AU - Kang, Kyo Bin

AU - Keefe, Christopher R.

AU - Keim, Paul

AU - Kelley, Scott T.

AU - Knights, Dan

AU - Koester, Irina

AU - Kosciolek, Tomasz

AU - Kreps, Jorden

AU - Langille, Morgan G.I.

AU - Lee, Joslynn

AU - Ley, Ruth

AU - Liu, Yong Xin

AU - Loftfield, Erikka

AU - Lozupone, Catherine

AU - Maher, Massoud

AU - Marotz, Clarisse

AU - Martin, Bryan D.

AU - McDonald, Daniel

AU - McIver, Lauren J.

AU - Melnik, Alexey V.

AU - Metcalf, Jessica L.

AU - Morgan, Sydney C.

AU - Morton, Jamie T.

AU - Naimey, Ahmad Turan

AU - Navas-Molina, Jose A.

AU - Nothias, Louis Felix

AU - Orchanian, Stephanie B.

AU - Pearson, Talima

AU - Peoples, Samuel L.

AU - Petras, Daniel

AU - Preuss, Mary Lai

AU - Pruesse, Elmar

AU - Rasmussen, Lasse Buur

AU - Rivers, Adam

AU - Robeson, Michael S.

AU - Rosenthal, Patrick

AU - Segata, Nicola

AU - Shaffer, Michael

AU - Shiffer, Arron

AU - Sinha, Rashmi

AU - Song, Se Jin

AU - Spear, John R.

AU - Swafford, Austin D.

AU - Thompson, Luke R.

AU - Torres, Pedro J.

AU - Trinh, Pauline

AU - Tripathi, Anupriya

AU - Turnbaugh, Peter J.

AU - Ul-Hasan, Sabah

AU - van der Hooft, Justin J.J.

AU - Vargas, Fernando

AU - Vázquez-Baeza, Yoshiki

AU - Vogtmann, Emily

AU - von Hippel, Max

AU - Walters, William

AU - Wan, Yunhu

AU - Wang, Mingxun

AU - Warren, Jonathan

AU - Weber, Kyle C.

AU - Williamson, Charles H.D.

AU - Willis, Amy D.

AU - Xu, Zhenjiang Zech

AU - Zaneveld, Jesse R.

AU - Zhang, Yilong

AU - Zhu, Qiyun

AU - Knight, Rob

AU - Caporaso, J. Gregory

N1 - Funding Information: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award. Thanks to the Yellowstone Center for Resources for research permit no. 5664 to J.R.S. for Yellowstone access and sample collection. We thank P. J. McMurdie for helpful discussion on the relationships between QIIME 2 and phyloseq. We would like to thank the users of QIIME 1 and 2, whose invaluable feedback has shaped QIIME 2. In particular, we would like to thank A. Abdelfattah (Stockholm University, Sweden), R. C. T. Boutin (University of British Columbia, Canada), D. J. Bradshaw II (Florida Atlantic University Harbor Branch Oceanographic Institute, USA), L. Bullington (MPG Ranch, USA), J. W. Debelius (Karolinska Institutet, Sweden), C. Duvallet (Massachusetts Institute of Technology, USA), E. Korzune Ganda (Cornell University, USA), A. Mahnert (Medical University of Graz, Austria), M. C. Melendrez (St. Cloud State University, USA), D. O’Rourke (University of New Hampshire, USA), A. R. Rivers (USDA ARS, USA), B. Sen (Tianjin University, China), S. Tangedal (Haukeland University Hospital and University of Bergen, Norway), P. J. Torres (San Diego State University, USA) and J. Warren (National Laboratory Service, UK) for writing end-user reviews included in the Supplementary Methods.

PY - 2019/8/1

Y1 - 2019/8/1

UR - http://www.scopus.com/inward/record.url?scp=85069676260&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85069676260&partnerID=8YFLogxK

U2 - 10.1038/s41587-019-0209-9

DO - 10.1038/s41587-019-0209-9

M3 - Letter

C2 - 31341288

AN - SCOPUS:85069676260

SN - 1087-0156

VL - 37

SP - 852

EP - 857

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 8

ER -

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

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