{"id":"W4416715660","doi":"10.1186/s40168-025-02240-5","title":"Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures","year":2025,"lang":"en","type":"article","venue":"Microbiome","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Lawson Health Research Institute; Western University","funders":"Vector Institute; Natural Sciences and Engineering Research Council of Canada; Mitacs","keywords":"Metagenomics; Microbiome; Confounding; Gut microbiome; Microbial ecology; Disease; Dysbiosis; Human disease","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":[0.0008161479,0.0004961752,0.0005205912,0.00141813,0.0003991872,0.00101572,0.0002733078,0.0004221614,0.001610569],"category_scores_gemma":[0.002321815,0.0001689479,0.0008085476,0.001319984,0.0005503697,0.000569626,0.001330285,0.0007878874,0.0003100141],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003944053,"about_ca_system_score_gemma":0.0004038036,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002091827,"about_ca_topic_score_gemma":0.003311058,"domain_scores_codex":[0.9994866,0.0001494634,0.0000348048,0.0002038886,0.00004930539,0.00007594813],"domain_scores_gemma":[0.9989809,0.0003788521,0.0003030608,0.000145962,0.00009809263,0.00009301628],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0008589698,0.00008899956,0.9171726,0.0002800492,0.0007820225,0.0001499844,0.0004111113,0.00571823,0.02547629,0.00089653,0.0008461068,0.04731911],"study_design_scores_gemma":[0.00002304568,0.0001703703,0.9498328,0.0001040867,0.0003352172,0.0004884321,0.0007447238,0.03190413,0.005156301,0.008546676,0.002646053,0.00004819626],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9824859,0.001455724,0.01166715,0.0002303837,0.00001320632,0.00001790137,0.003120864,0.00008724652,0.0009216111],"genre_scores_gemma":[0.9931527,0.0002465791,0.004558027,0.0000844631,0.000008824049,0.00002061003,0.001770488,0.00001920134,0.0001391088],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002091827,"threshold_uncertainty_score":0.005387902,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01373111745098192,"score_gpt":0.2570806856518162,"score_spread":0.2433495682008343,"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."}}