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Characterization of the microbiome and immune response in corals with chronic Montipora white syndrome.

Autor: Brown T; School of Aquatic and Fisheries Sciences, University of Washington, Seattle, Washington, USA., Sonett D; Division of Biological Sciences, University of Washington, Bothell, Washington, USA., Zaneveld JR; Division of Biological Sciences, University of Washington, Bothell, Washington, USA., Padilla-Gamiño JL; School of Aquatic and Fisheries Sciences, University of Washington, Seattle, Washington, USA.

Publikováno v: Molecular ecology [Mol Ecol] 2021 Jun; Vol. 30 (11), pp. 2591-2606. Date of Electronic Publication: 2021 May 02.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Autor: 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.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2019 Sep; Vol. 37 (9), pp. 1091.

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny.

Autor: Pollock FJ; Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, State College, PA, 16802, USA., McMinds R; Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA., Smith S; Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, State College, PA, 16802, USA., Bourne DG; College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.; Australian Institute of Marine Science, Townsville, QLD, 4810, Australia., Willis BL; College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia., Medina M; Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, State College, PA, 16802, USA.; Smithsonian Tropical Research Institute, Smithsonian Institution, 9100 Panama City PL, Washington, DC, 20521, USA., Thurber RV; Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA., Zaneveld JR; Division of Biological Sciences, Bothell, School of Science, Technology, Engineering, and Mathematics, University of Washington, UWBB-277, Bothell, WA, 98011, USA. zaneveld@gmail.com.

Publikováno v: Nature communications [Nat Commun] 2018 Nov 22; Vol. 9 (1), pp. 4921. Date of Electronic Publication: 2018 Nov 22.

Best practices for analysing microbiomes.

Autor: Knight R; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu., Vrbanac A; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA., Taylor BC; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA., Aksenov A; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Callewaert C; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.; Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium., Debelius J; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA., Gonzalez A; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA., Kosciolek T; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA., McCall LI; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., McDonald D; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA., Melnik AV; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Morton JT; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA., Navas J; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA., Quinn RA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Sanders JG; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 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.; Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, La Jolla, CA, USA., Tripathi A; Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA., Xu ZZ; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA., Zaneveld JR; Division of Biological Sciences, School of Science Technology Engineering and Math, University of Washington Bothell, Bothell, WA, USA., Zhu Q; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA., Caporaso JG; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA., Dorrestein PC; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.

Publikováno v: Nature reviews. Microbiology [Nat Rev Microbiol] 2018 Jul; Vol. 16 (7), pp. 410-422.