{"id":"W4413361880","doi":"10.1101/2025.08.19.671110","title":"A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on Hyphomicrobiales dark matter","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Phyllosphere; Metagenomics; Diversity (politics); Dark matter; Biology; Evolutionary biology; Ecology; Computational biology; Physics; Sociology; Bacteria; Paleontology; Particle physics; Genetics; Anthropology; Gene","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":[0.0007595429,0.0007205973,0.0007000797,0.001390911,0.0005194096,0.00131942,0.0004186231,0.0006037646,0.0006565433],"category_scores_gemma":[0.0005500674,0.0002915562,0.001055845,0.001174337,0.0002347971,0.0006870021,0.0008400885,0.0006663485,0.0003386303],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003007247,"about_ca_system_score_gemma":0.0005124164,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001726803,"about_ca_topic_score_gemma":0.002395809,"domain_scores_codex":[0.9993908,0.0001260948,0.00003850834,0.0001926545,0.0001525378,0.00009941377],"domain_scores_gemma":[0.9997173,0.00005621881,0.00005588578,0.00004673388,0.00007889723,0.00004489367],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"meta_analysis","study_design_scores_codex":[0.0003953375,0.0001383771,0.06428492,0.0003872948,0.0006587321,0.0001468115,0.0002954414,0.001459813,0.9089928,0.0002538212,0.0003022097,0.02268451],"study_design_scores_gemma":[0.00004055072,0.001004515,0.6477646,0.0003051204,0.001566445,0.0007590867,0.002479572,0.03993573,0.2914335,0.001905789,0.01266827,0.0001368673],"study_design_candidate":"meta_analysis","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9813305,0.002354352,0.01069765,0.0002843676,0.00002451321,0.00004889412,0.004134288,0.0001876838,0.0009377498],"genre_scores_gemma":[0.9811056,0.0008196603,0.01372436,0.0001594087,0.0000134295,0.00005092199,0.003520907,0.00005890909,0.0005467716],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001726803,"threshold_uncertainty_score":0.004016876,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02967370565283332,"score_gpt":0.2204061758386237,"score_spread":0.1907324701857903,"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."}}