{"id":"W3094098795","doi":"10.3389/fmicb.2020.586387","title":"Microbiome Profiling Reveals a Microbial Dysbiosis During a Natural Outbreak of Tenacibaculosis (Yellow Mouth) in Atlantic Salmon","year":2020,"lang":"en","type":"article","venue":"Frontiers in Microbiology","topic":"Aquaculture disease management and microbiota","field":"Immunology and Microbiology","cited_by":58,"is_retracted":false,"has_abstract":true,"ca_institutions":"Cermaq (Canada); BC Centre for Aquatic Health Sciences; University of Prince Edward Island","funders":"Commonwealth Scientific and Industrial Research Organisation","keywords":"Biology; Dysbiosis; Vibrio; Microbiome; Zoology; Relative species abundance; Metagenomics; Microbial population biology; Aquaculture; Amplicon sequencing; Abundance (ecology); Outbreak; Ecology; Microbiology; 16S ribosomal RNA; Fish <Actinopterygii>; Bacteria; Fishery; Genetics; Gene","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003224231,0.0006356528,0.001383142,0.0007344725,0.0001122583,0.00002204114,0.0008425848,0.0006911745,0.0001424632],"category_scores_gemma":[0.000130482,0.0005983032,0.0003754296,0.0009978068,0.0004732053,0.0001628405,0.0004792421,0.000822411,0.0001685849],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002173916,"about_ca_system_score_gemma":0.00007169232,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001825158,"about_ca_topic_score_gemma":0.00009259688,"domain_scores_codex":[0.995919,0.0004862939,0.001262802,0.001137393,0.00003387358,0.001160674],"domain_scores_gemma":[0.9989211,0.00005480808,0.0004444813,0.0004247387,0.00008757097,0.00006732533],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001091309,0.0002395845,0.08524916,0.0003875413,0.0003370204,0.00005979479,0.001419485,0.00001106388,0.8967784,0.00002954815,0.01419012,0.0002069846],"study_design_scores_gemma":[0.0116934,0.0002645104,0.01917632,0.0005632947,0.0003138079,0.0001846956,0.003369889,0.00002374528,0.952616,0.00005241267,0.01019632,0.001545585],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9903437,0.005389442,0.00008340065,0.001025926,0.001389305,0.001160049,0.0003668108,0.0001029252,0.0001384406],"genre_scores_gemma":[0.9946908,0.0001739272,0.002175972,0.0005996753,0.00006477218,0.00003987049,0.001429872,0.0000624236,0.0007626395],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06607284,"threshold_uncertainty_score":0.9996468,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006539022671593825,"score_gpt":0.2009020881892801,"score_spread":0.1943630655176863,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}