{"id":"W4409527835","doi":"10.1093/ismejo/wraf071","title":"Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis","year":2025,"lang":"en","type":"article","venue":"The ISME Journal","topic":"Evolution and Genetic Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Linacre College, University of Oxford","keywords":"Biology; Pathogen; Virulence; Dysbiosis; Microbiology; Host (biology); Metagenomics; Microbiome; Genetics; Gene","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003004041,0.0002511195,0.0002327889,0.0002746528,0.0003114969,0.0007092384,0.0002600714,0.0005331028,0.0008937948],"category_scores_gemma":[0.0003803125,0.000169418,0.0001823397,0.000244786,0.0004346284,0.0004484071,0.0007639891,0.0006167449,0.0002248874],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004341055,"about_ca_system_score_gemma":0.000341141,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004065398,"about_ca_topic_score_gemma":0.0008536925,"domain_scores_codex":[0.9997546,0.00004118909,0.00001018296,0.00006774838,0.00005633189,0.00006995043],"domain_scores_gemma":[0.9997368,0.00004456812,0.00009452515,0.00003332371,0.0000271843,0.00006358126],"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":[0.00006449244,0.00004108743,0.006144576,0.00003074695,0.00001786527,0.0002178699,0.00005664098,0.0003951492,0.9854221,0.001325754,0.000106381,0.006177249],"study_design_scores_gemma":[0.00004951283,0.0008537734,0.3443194,0.00005005645,0.0001093384,0.005925627,0.00113983,0.04237744,0.5810606,0.008735685,0.0152843,0.00009450442],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9948402,0.0005053631,0.003001844,0.0001802706,0.00001456497,0.000006404926,0.00005218829,0.00003723697,0.001361966],"genre_scores_gemma":[0.9979583,0.0002008642,0.001242586,0.00006826264,0.000005489141,0.000005618235,0.00004371655,0.00001033676,0.0004648681],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0008937948,"threshold_uncertainty_score":0.003149629,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.003150307946663747,"score_gpt":0.2220412950773596,"score_spread":0.2188909871306959,"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."}}