{"id":"W3104596207","doi":"10.1038/s41587-020-0718-6","title":"A genomic catalog of Earth’s microbiomes","year":2020,"lang":"en","type":"article","venue":"Nature Biotechnology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":973,"is_retracted":false,"has_abstract":true,"ca_institutions":"Concordia University; University of Windsor; University of Waterloo; Geological Survey of Canada; Natural Resources Canada; University of Calgary; Agriculture and Agri-Food Canada; University of British Columbia; Institut National de la Recherche Scientifique; University of Toronto; McMaster University","funders":"Lawrence Livermore National Laboratory; Mikrobiologický Ústav, Akademie Věd České Republiky; Agriculture and Agri-Food Canada; Sandia National Laboratories; Great Lakes Bioenergy Research Center; Natural Resources Canada; School of Life Sciences, Arizona State University; University of Oregon; Advanced Research Projects Agency - Energy; Stockholms Universitet; College of Engineering, Michigan State University; Addis Ababa University; North Carolina State University; University of Washington; Linnéuniversitetet; Universidad de Buenos Aires; Office of Science; Max-Planck-Institut für Terrestrische Mikrobiologie; Akademie Věd České Republiky; Universität Wien; Georgia Institute of Technology; Consejo Nacional de Investigaciones Científicas y Técnicas; Baqiyatallah University of Medical Sciences; University of Toronto; University of New South Wales; National Energy Research Scientific Computing Center; Directorate for Biological Sciences; Joint Genome Institute; University of Waikato; Oregon State University; Montana State University; Koninklijk Nederlands Instituut voor Onderzoek der Zee; West Virginia University; University of California, San Diego; University of Montana; University of Arkansas for Medical Sciences; Pennsylvania State University; Michigan State University; McMaster University; University of California, Davis; University of Akron; Harvard University; Science for Life Laboratory; Universiteit Utrecht; University of Minnesota; Oklahoma State University; AgResearch; Arizona State University; Division of Ocean Sciences; University of Wisconsin-Madison; U.S. Department of Energy; Sveriges Lantbruksuniversitet; Lembaga Ilmu Pengetahuan Indonesia; Aarhus Universitet; Ohio State University; Clemson University; Louisiana State University; Colorado State University","keywords":"Metagenomics; Biology; Microbiome; Phylum; Genome; Microbial ecology; Archaea; Evolutionary biology; Ecology; Computational biology; Phylogenetic tree; Extant taxon; Host (biology); Bacteria; Gene; Genetics","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006102473,0.0005729072,0.0007101592,0.00887159,0.000882833,0.001746019,0.000446078,0.0004796834,0.004832193],"category_scores_gemma":[0.002553758,0.0003135946,0.0004900955,0.0146854,0.0003314309,0.001237806,0.001514954,0.0006015544,0.002880544],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004203722,"about_ca_system_score_gemma":0.002077991,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004330614,"about_ca_topic_score_gemma":0.004471136,"domain_scores_codex":[0.9995572,0.00003829595,0.00005968263,0.0001411715,0.0001332935,0.00007027586],"domain_scores_gemma":[0.9983414,0.0002554996,0.0002549497,0.0002832784,0.000555663,0.0003091465],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"observational","study_design_scores_codex":[0.001007213,0.0001453221,0.09072939,0.005620756,0.0002551689,0.001594312,0.003967816,0.003012275,0.2057225,0.02125232,0.09384998,0.572843],"study_design_scores_gemma":[0.00004260294,0.0001435557,0.2055749,0.0007634246,0.0001505618,0.001525293,0.001331934,0.001158041,0.009954189,0.006987096,0.7722848,0.00008353733],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"dataset","genre_gemma":"empirical","genre_scores_codex":[0.2790195,0.02360754,0.02054838,0.00136344,0.0002439186,0.0002428498,0.6446863,0.00255389,0.02773423],"genre_scores_gemma":[0.14325,0.0125443,0.05076667,0.0006855755,0.0001817951,0.0002641897,0.7870142,0.0004955257,0.004797574],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.00887159,"threshold_uncertainty_score":0.01616526,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005294096201759396,"score_gpt":0.2089388733343887,"score_spread":0.2036447771326293,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). 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