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

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

doi:10.1038/s41587-019-0209-9

Rapid advances in DNA-sequencing and bioinformatics technologies in the past two decades have substantially improved understanding of the microbial world. This growing understanding relates to the vast diversity of microorganisms; how microbiota and microbiomes affect disease and medical treatment; how microorganisms affect the health of the planet; and the nascent exploration of the medical, forensic, environmental and agricultural applications of microbiome biotechnology. Much of this work has been driven by marker-gene surveys (for example, bacterial/archaeal 16S rRNA genes, fungal internal-transcribed-spacer regions and eukaryotic 18S rRNA genes), which profile microbiota with varying degrees of taxonomic specificity and phylogenetic information. The field is now transitioning to integrate other data types, such as metabolite, metaproteome or metatranscriptome profiles.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 / Bolyen, Evan; Rideout, Jai Ram; Dillon, Matthew R.; Bokulich, Nicholas A.; Abnet, Christian C.; Al-Ghalith, Gabriel A.; Alexander, Harriet; Alm, Eric J.; Arumugam, Manimozhiyan; Asnicar, Francesco; Bai, Yang; Bisanz, Jordan E.; Bittinger, Kyle; Brejnrod, Asker; Brislawn, Colin J.; Brown, C. Titus; Callahan, Benjamin J.; Caraballo-Rodríguez, Andrés Mauricio; Chase, John; Cope, Emily K.; Da Silva, Ricardo; Diener, Christian; Dorrestein, Pieter C.; Douglas, Gavin M.; Durall, Daniel M.; Duvallet, Claire; Edwardson, Christian F.; Ernst, Madeleine; Estaki, Mehrbod; Fouquier, Jennifer; Gauglitz, Julia M.; Gibbons, Sean M.; Gibson, Deanna L.; Gonzalez, Antonio; Gorlick, Kestrel; Guo, Jiarong; Hillmann, Benjamin; Holmes, Susan; Holste, Hannes; Huttenhower, Curtis; Huttley, Gavin A.; Janssen, Stefan; Jarmusch, Alan K.; Jiang, Lingjing; Kaehler, Benjamin D.; Kang, Kyo Bin; Keefe, Christopher R.; Keim, Paul; Kelley, Scott T.; Knights, Dan; Koester, Irina; Kosciolek, Tomasz; Kreps, Jorden; Langille, Morgan G. I.; Lee, Joslynn; Ley, Ruth; Liu, Yong-Xin; Loftfield, Erikka; Lozupone, Catherine; Maher, Massoud; Marotz, Clarisse; Martin, Bryan D.; Mcdonald, Daniel; Mciver, Lauren J.; Melnik, Alexey V.; Metcalf, Jessica L.; Morgan, Sydney C.; Morton, Jamie T.; Naimey, Ahmad Turan; Navas-Molina, Jose A.; Nothias, Louis Felix; Orchanian, Stephanie B.; Pearson, Talima; Peoples, Samuel L.; Petras, Daniel; Preuss, Mary Lai; Pruesse, Elmar; Rasmussen, Lasse Buur; Rivers, Adam; Robeson, Michael S.; Rosenthal, Patrick; Segata, Nicola; Shaffer, Michael; Shiffer, Arron; Sinha, Rashmi; Song, Se Jin; Spear, John R.; Swafford, Austin D.; Thompson, Luke R.; Torres, Pedro J.; Trinh, Pauline; Tripathi, Anupriya; Turnbaugh, Peter J.; Ul-Hasan, Sabah; van der Hooft, Justin J. J.; Vargas, Fernando; Vázquez-Baeza, Yoshiki; Vogtmann, Emily; von Hippel, Max; Walters, William; Wan, Yunhu; Wang, Mingxun; Warren, Jonathan; Weber, Kyle C.; Williamson, Charles H. D.; Willis, Amy D.; Xu, Zhenjiang Zech; Zaneveld, Jesse R.; Zhang, Yilong; Zhu, Qiyun; Knight, Rob; Caporaso, J. Gregory. - In: NATURE BIOTECHNOLOGY. - ISSN 1087-0156. - 37:8(2019), pp. 852-857. [10.1038/s41587-019-0209-9]