تقرير
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
| العنوان: | Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. |
|---|---|
| المؤلفون: | Bolyen E; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Rideout JR; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Dillon MR; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Bokulich NA; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Abnet CC; Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA., Al-Ghalith GA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA., Alexander H; Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.; Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA., Alm EJ; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA., Arumugam M; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., Asnicar F; Centre for Integrative Biology, University of Trento, Trento, Italy., Bai Y; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China.; University of Chinese Academy of Sciences, Beijing, China., Bisanz JE; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA., Bittinger K; Division of Gastroenterology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Hepatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA., Brejnrod A; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., Brislawn CJ; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA., Brown CT; Department of Population Health and Reproduction, University of California, Davis, Davis, CA, USA., Callahan BJ; Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA.; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA., Caraballo-Rodríguez AM; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Chase J; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Cope EK; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA., Da Silva R; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Diener C; Institute for Systems Biology, Seattle, WA, USA., Dorrestein PC; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Douglas GM; Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada., Durall DM; Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada., Duvallet C; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA., Edwardson CF; A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA., Ernst M; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark., Estaki M; Department of Biology, University of British Columbia Okanagan, Okanagan, British Columbia, Canada., Fouquier J; Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Gauglitz JM; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Gibbons SM; Institute for Systems Biology, Seattle, WA, USA.; eScience Institute, University of Washington, Seattle, WA, USA., Gibson DL; Irving K. Barber School of Arts and Sciences, Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.; Department of Medicine, University of British Columbia, Kelowna, British Columbia, Canada., Gonzalez A; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Gorlick K; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Guo J; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA., Hillmann B; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA., Holmes S; Statistics Department, Stanford University, Palo Alto, CA, USA., Holste H; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA., Huttenhower C; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Huttley GA; Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia., Janssen S; Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany., Jarmusch AK; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Jiang L; Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA., Kaehler BD; Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.; School of Science, University of New South Wales, Canberra, Australian Capital Territory, Australia., Kang KB; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea., Keefe CR; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Keim P; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Kelley ST; Department of Biology, San Diego State University, San Diego, CA, USA., Knights D; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.; Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA., Koester I; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Kosciolek T; Department of Pediatrics, University of California San Diego, La Jolla, California, USA., Kreps J; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Langille MGI; Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada., Lee J; Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA., Ley R; Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA., Liu YX; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China., Loftfield E; Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA., Lozupone C; Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Maher M; Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA., Marotz C; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Martin BD; Department of Statistics, University of Washington, Seattle, WA, USA., McDonald D; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., McIver LJ; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Melnik AV; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Metcalf JL; Department of Animal Science, Colorado State University, Fort Collins, CO, USA., Morgan SC; Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, British Columbia, Canada., Morton JT; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA., Naimey AT; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Navas-Molina JA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.; Google LLC, Mountain View, CA, USA., Nothias LF; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Orchanian SB; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Pearson T; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Peoples SL; School of Information Studies, Syracuse University, Syracuse, NY, USA.; School of STEM, University of Washington Bothell, Bothell, WA, USA., Petras D; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Preuss ML; Department of Biological Sciences, Webster University, St. Louis, MO, USA., Pruesse E; Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Rasmussen LB; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., Rivers A; Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA., Robeson MS 2nd; College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA., Rosenthal P; Department of Biological Sciences, Webster University, St. Louis, MO, USA., Segata N; Centre for Integrative Biology, University of Trento, Trento, Italy., Shaffer M; Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.; Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA., Shiffer A; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Sinha R; Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA., Song SJ; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Spear JR; Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA., Swafford AD; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Thompson LR; Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA.; Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA., Torres PJ; Department of Biology, San Diego State University, San Diego, CA, USA., Trinh P; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA., Tripathi A; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Division of Biological Sciences, University of California San Diego, San Diego, CA, USA., Turnbaugh PJ; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA., Ul-Hasan S; Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA., van der Hooft JJJ; Bioinformatics Group, Wageningen University, Wageningen, the Netherlands., Vargas F; Division of Biological Sciences, University of California San Diego, San Diego, CA, USA., Vázquez-Baeza Y; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Vogtmann E; Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA., von Hippel M; Department of Mathematics, University of Arizona, Tucson, AZ, USA., Walters W; Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany., Wan Y; Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA., Wang M; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Warren J; National Laboratory Service, Environment Agency, Starcross, UK., Weber KC; Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA.; College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA., Williamson CHD; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Willis AD; Department of Biostatistics, University of Washington, Seattle, WA, USA., Xu ZZ; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Zaneveld JR; School of STEM, Division of Biological Sciences, University of Washington Bothell, Bothell, WA, USA., Zhang Y; Merck & Co. Inc., Kenilworth, NJ, USA., Zhu Q; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Knight R; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA., Caporaso JG; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu.; Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA. greg.caporaso@nau.edu. |
| المصدر: | Nature biotechnology [Nat Biotechnol] 2019 Aug; Vol. 37 (8), pp. 852-857. |
| نوع المنشور: | Letter; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: New York Ny : Nature America Publishing Original Publication: New York, NY : Nature Pub. Co., [1996- |
| مواضيع طبية MeSH: | Computational Biology* , Data Science* , Microbiota* , Software*, Databases, Factual ; Humans |
| التعليقات: | Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6. (PMID: 31399723) |
| References: | Science. 2013 Feb 1;339(6119):548-54. (PMID: 23363771) Gigascience. 2012 Jul 12;1(1):7. (PMID: 23587224) Nat Methods. 2016 Jul;13(7):581-3. (PMID: 27214047) Science. 2016 Jan 8;351(6269):158-62. (PMID: 26657285) Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):11169-11174. (PMID: 28973879) Nat Methods. 2018 Oct;15(10):796-798. (PMID: 30275573) Nat Methods. 2018 Nov;15(11):962-968. (PMID: 30377376) Gut Microbes. 2018 Jul 4;9(4):338-356. (PMID: 29517944) Nat Methods. 2015 Feb;12(2):115-21. (PMID: 25633503) ISME J. 2009 Feb;3(2):179-89. (PMID: 18971961) Sci Rep. 2018 Feb 27;8(1):3669. (PMID: 29487294) Appl Environ Microbiol. 2009 Dec;75(23):7537-41. (PMID: 19801464) PLoS One. 2013 Apr 22;8(4):e61217. (PMID: 23630581) Trends Plant Sci. 2017 Sep;22(9):770-778. (PMID: 28757147) Ecol Appl. 2018 Sep;28(6):1594-1605. (PMID: 29989265) Science. 2018 Jan 5;359(6371):97-103. (PMID: 29097493) Nat Biotechnol. 2016 Aug 9;34(8):828-837. (PMID: 27504778) Nat Methods. 2015 Oct;12(10):902-3. (PMID: 26418763) Microbiome. 2018 May 17;6(1):90. (PMID: 29773078) Front Cell Infect Microbiol. 2018 May 23;8:168. (PMID: 29876323) Nat Biotechnol. 2013 Sep;31(9):814-21. (PMID: 23975157) Ecology. 2017 Mar;98(3):616-623. (PMID: 27984635) |
| معلومات مُعتمدة: | R35 GM133420 United States GM NIGMS NIH HHS; U54 MD012388 United States MD NIMHD NIH HHS; U54 CA143925 United States CA NCI NIH HHS; T32 ES015459 United States ES NIEHS NIH HHS; Z99 CA999999 United States ImNIH Intramural NIH HHS |
| تواريخ الأحداث: | Date Created: 20190726 Date Completed: 20191106 Latest Revision: 20240725 |
| رمز التحديث: | 20240726 |
| مُعرف محوري في PubMed: | PMC7015180 |
| DOI: | 10.1038/s41587-019-0209-9 |
| PMID: | 31341288 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1546-1696 |
|---|---|
| DOI: | 10.1038/s41587-019-0209-9 |