{"id":"W4319655962","doi":"10.7554/elife.78530","title":"Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome","year":2023,"lang":"en","type":"article","venue":"eLife","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":25,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Université de Montréal","funders":"National Institute of Mental Health; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs; National Institutes of Health; Research Corporation for Science Advancement","keywords":"Biology; Alpha diversity; Microbiome; Nucleotide diversity; Ecology; Genetic diversity; Beta diversity; Evolutionary biology; Ecosystem diversity; Species diversity; Biodiversity; Genetics; Gene; Population; Allele","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":[0.0005042275,0.000174202,0.0003469364,0.0009051425,0.000346529,0.0005439545,0.0001735691,0.0004522641,0.001282978],"category_scores_gemma":[0.002169105,0.0002019869,0.0002983917,0.0008809143,0.0004459998,0.0004461065,0.0007652467,0.0005559532,0.0002314764],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00016206,"about_ca_system_score_gemma":0.0001314994,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001272986,"about_ca_topic_score_gemma":0.00189698,"domain_scores_codex":[0.999532,0.0001046078,0.00003012207,0.0001733296,0.00008868257,0.00007136046],"domain_scores_gemma":[0.9984517,0.000304328,0.000699206,0.0001349097,0.0001846947,0.0002251518],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003820943,0.00005123957,0.9650039,0.00007897695,0.0001933737,0.0001367589,0.0002804907,0.0002170269,0.02391974,0.00009449536,0.0001858728,0.009455964],"study_design_scores_gemma":[0.000001774464,0.00006110883,0.9981499,0.000008235261,0.0000175697,0.0003002955,0.0001567919,0.0002779567,0.0006772,0.0001889511,0.0001539666,0.000006254102],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.99768,0.00113624,0.000567267,0.00007518525,0.000006051484,0.000003582734,0.0002381945,0.000009004157,0.0002844278],"genre_scores_gemma":[0.999057,0.0002106147,0.000356444,0.00004274509,0.000008556308,0.000005415792,0.0001877245,0.000004136826,0.0001273618],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001282978,"threshold_uncertainty_score":0.004292011,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03053159211792205,"score_gpt":0.248340637678588,"score_spread":0.217809045560666,"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."}}