{"id":"W4410280320","doi":"10.1080/19490976.2025.2501492","title":"Bacteriophage-driven DNA inversions shape bacterial functionality and long-term co-existence in <i>Bacteroides fragilis</i>","year":2025,"lang":"en","type":"article","venue":"Gut Microbes","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Institute for Advanced Research","funders":"Technion-Israel Institute of Technology; European Research Council; Human Frontier Science Program; European Commission; Canadian Institute for Advanced Research; Israel Institute; University of Michigan; Seerave Foundation; Israel Cancer Research Fund","keywords":"Bacteroides fragilis; Biology; Bacteriophage; DNA; Term (time); Microbiology; Bacteriophage Mu; Genetics; Computational biology; Bacteria; Gene; Escherichia coli","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":[0.00008109212,0.0002078775,0.0001025634,0.0001400319,0.00008734619,0.0001937447,0.0001076517,0.0001865204,0.0005887179],"category_scores_gemma":[0.0001261968,0.00007940966,0.0001076461,0.00008208566,0.000150042,0.0001149304,0.0002126534,0.0002668246,0.0001495019],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001975164,"about_ca_system_score_gemma":0.00008361548,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004853499,"about_ca_topic_score_gemma":0.0006343519,"domain_scores_codex":[0.9998989,0.00001509765,0.000004389286,0.00002056936,0.0000216654,0.00003928046],"domain_scores_gemma":[0.9998928,0.00001470387,0.00004620316,0.000008022866,0.000009477701,0.00002866555],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00004213898,0.000004774346,0.0003249317,0.000004128843,8.128747e-7,0.00001061667,0.000007870748,0.00001105825,0.9992937,0.000009538559,0.000005721713,0.0002846505],"study_design_scores_gemma":[0.00001040556,0.0006566645,0.09674339,0.000008081804,0.00001189296,0.0002982146,0.0001525935,0.001133295,0.8998472,0.00007356114,0.00105087,0.0000137463],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9992874,0.0001242593,0.000296745,0.00001522815,0.000002902878,0.000002890814,0.00006355637,0.00001432199,0.0001927316],"genre_scores_gemma":[0.9992698,0.00004638291,0.0002366818,0.00001244936,0.000001923556,0.000005542063,0.0001035136,0.000005217131,0.0003185868],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0005887179,"threshold_uncertainty_score":0.001969457,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01020416750639932,"score_gpt":0.2505172057294079,"score_spread":0.2403130382230086,"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."}}