{"id":"W4407355947","doi":"10.1186/s40168-025-02028-7","title":"The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency","year":2025,"lang":"en","type":"article","venue":"Microbiome","topic":"Immunodeficiency and Autoimmune Disorders","field":"Immunology and Microbiology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity; Université de Montréal; Montreal Clinical Research Institute","funders":"NHLBI Division of Intramural Research; National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; Canadian Institutes of Health Research; Bundesministerium für Bildung und Forschung; Institut de Recherche Clinique De Montréal; Tokyo Medical and Dental University; Università degli Studi di Brescia; Medizinische Fakultät der Albert-Ludwigs-Universität Freiburg; Universitätsklinikum Regensburg; Sungkyunkwan University; Albert-Ludwigs-Universität Freiburg; National Institutes of Health; Deutsche Forschungsgemeinschaft; Université de Liège; Wilhelm Sander-Stiftung","keywords":"Metabolome; Microbiome; Immunology; Biology; Immune dysregulation; Dysbiosis; Immune system; Common variable immunodeficiency; Disease; Immunodeficiency; Medical microbiology; Cytotoxic T cell; Metabolomics; Gut flora; Medicine; Internal medicine; Genetics; Bioinformatics; Antibody","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":[0.0002703441,0.0004109729,0.0004148783,0.0008234469,0.000322853,0.0005936006,0.0001464894,0.0004664146,0.00112359],"category_scores_gemma":[0.0007336651,0.0001861173,0.0002524213,0.00046322,0.0002129363,0.0002744089,0.0007032831,0.0003580642,0.0001868898],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002729139,"about_ca_system_score_gemma":0.0001266927,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001867249,"about_ca_topic_score_gemma":0.002535706,"domain_scores_codex":[0.9998347,0.00004039034,0.00001476191,0.00005654622,0.00002074876,0.00003288841],"domain_scores_gemma":[0.9997445,0.00004269356,0.0001007136,0.00001391968,0.00003460966,0.00006361322],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.002006832,0.0001454168,0.9637401,0.0000722977,0.0001638442,0.0002361302,0.0002938995,0.0001303242,0.02483154,0.00004162805,0.0002867338,0.008051255],"study_design_scores_gemma":[0.00002123979,0.0004580112,0.9959018,0.00003154351,0.00008648616,0.0006145887,0.0003395632,0.0005127863,0.001407012,0.00009732482,0.0005213361,0.000008404421],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9987825,0.0004001005,0.0001630809,0.00002192427,0.000004249663,0.00001326676,0.000390633,0.00000489066,0.0002192713],"genre_scores_gemma":[0.9984364,0.0001819817,0.0005023952,0.00004453515,0.000005332868,0.00002051803,0.000567045,0.000005080676,0.0002367507],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001867249,"threshold_uncertainty_score":0.003758729,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004495753309750517,"score_gpt":0.2143984244110372,"score_spread":0.2099026711012867,"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."}}