{"id":"W4396562295","doi":"10.1093/ismeco/ycae063","title":"Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes","year":2024,"lang":"en","type":"article","venue":"ISME Communications","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"National Institute of Allergy and Infectious Diseases; National Institute on Aging; Ontario Genomics; National Institutes of Health; Government of Canada; Genome Canada; Ontario Genomics Institute; University of Ottawa; Natural Sciences and Engineering Research Council of Canada; Eunice Kennedy Shriver National Institute of Child Health and Human Development; U.S. Department of Defense; Broad Institute; National Heart, Lung, and Blood Institute","keywords":"Metaproteomics; Metagenomics; Biology; Ecological niche; Microbiome; Computational biology; Niche; Proteome; Ecology; Gene; Evolutionary biology; Bioinformatics; Genetics; Habitat","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003056992,0.0001032044,0.0001902296,0.0000613351,0.0001121291,0.00004699699,0.000270084,0.00009090634,0.00000636798],"category_scores_gemma":[0.00003876325,0.00009557613,0.00005294994,0.00009375063,0.0001666798,0.000005807583,0.0006197621,0.0001002065,0.000003650686],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006924609,"about_ca_system_score_gemma":0.00005972988,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004325125,"about_ca_topic_score_gemma":0.00009356186,"domain_scores_codex":[0.9992885,0.0001024911,0.0002298033,0.0002195297,0.00002612966,0.0001335604],"domain_scores_gemma":[0.9991715,0.00003950537,0.00004707473,0.0006288671,0.00004074645,0.00007232853],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.000006758628,0.00004070195,0.0004989745,0.00005670193,0.00008378462,2.13786e-7,0.0001891635,5.685338e-7,0.9946361,0.002684808,0.0001437546,0.001658526],"study_design_scores_gemma":[0.0004156918,0.000194029,0.2950718,0.00006462821,0.000300461,0.00006881006,0.0002283931,0.0001559534,0.3148827,0.0008239286,0.3873402,0.000453371],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9821423,0.01363973,0.0004873382,0.003184352,0.00005152872,0.0002489813,0.0001335127,0.00001560315,0.00009662972],"genre_scores_gemma":[0.976007,0.007439502,0.01596106,0.0002847503,0.00002853719,0.00002735639,0.0001159721,0.00001257581,0.0001232248],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6797533,"threshold_uncertainty_score":0.3897482,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03595318457325334,"score_gpt":0.3067575061068869,"score_spread":0.2708043215336335,"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."}}