{"id":"W4409276842","doi":"10.1186/s40168-025-02091-0","title":"A blueprint for contemporary studies of microbiomes","year":2025,"lang":"en","type":"editorial","venue":"Microbiome","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":36,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Deutsche Forschungsgemeinschaft","keywords":"Microbiome; Biology; Blueprint; Microbial ecology; Medical microbiology; Computational biology; Evolutionary biology; Bioinformatics; Microbiology; Genetics; Bacteria; Engineering","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"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":[0.000427532,0.0004684628,0.0009139507,0.0002668416,0.0001060801,0.00002176806,0.0005315353,0.001147057,0.000006610297],"category_scores_gemma":[0.0003527061,0.0004534234,0.0004404906,0.0001655968,0.0002909723,0.000002441494,0.0004307633,0.000241383,0.000008203717],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007546355,"about_ca_system_score_gemma":0.001496971,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000463049,"about_ca_topic_score_gemma":0.00003777305,"domain_scores_codex":[0.9978775,0.00007204078,0.0007368514,0.0007966929,0.00009790285,0.0004189779],"domain_scores_gemma":[0.9978573,0.0001560609,0.0004466436,0.000695047,0.0007827937,0.00006214537],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001256796,0.00005771187,0.000003471683,0.001518159,0.0003684133,7.229246e-7,0.0000430668,1.955496e-7,0.4871709,0.000005880712,0.5105872,0.0001185883],"study_design_scores_gemma":[0.001056247,0.0002877561,0.000004037082,0.0003730561,0.00007110984,0.000001867946,0.00007444381,9.712101e-8,0.2272648,0.00002307362,0.770537,0.0003064918],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"editorial","genre_gemma":"editorial","genre_scores_codex":[0.01073325,0.06011923,0.0004264156,0.0003729897,0.9133648,0.002133525,0.01232369,0.00004681019,0.0004793491],"genre_scores_gemma":[0.01562524,0.01012688,0.007697775,0.0008258175,0.8619674,0.0004979438,0.03481206,0.0003370692,0.06810985],"genre_candidate":"editorial","genre_consensus":"editorial","teacher_disagreement_score":0.2599498,"threshold_uncertainty_score":0.9997917,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02451546036844778,"score_gpt":0.3494278378490833,"score_spread":0.3249123774806356,"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."}}