{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002702736,0.001452629,0.001187468,0.00284609,0.0006431693,0.001777604,0.0007676281,0.0009344999,0.00116713],"category_scores_gemma":[0.004533516,0.0007100388,0.002240742,0.001922656,0.0005299879,0.001399177,0.00175762,0.001098771,0.0004002839],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007074795,"about_ca_system_score_gemma":0.001379959,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001894039,"about_ca_topic_score_gemma":0.002592393,"domain_scores_codex":[0.9992017,0.0002845434,0.00004458685,0.0002511767,0.0001425649,0.00007547779],"domain_scores_gemma":[0.9983454,0.0008429344,0.0002195062,0.0002630219,0.0001737033,0.0001554442],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.002017357,0.001130469,0.2796378,0.001343748,0.0039311,0.0004738253,0.00041667,0.2377796,0.3710143,0.005320389,0.001745386,0.09518941],"study_design_scores_gemma":[0.00006298602,0.0002855118,0.05042036,0.00003630789,0.0003040823,0.0001694162,0.0001586582,0.8938913,0.04300293,0.009824447,0.00175245,0.00009152987],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6359097,0.001107039,0.3529415,0.0006059012,0.00006494148,0.000199473,0.005076525,0.002696736,0.001398108],"genre_scores_gemma":[0.8154054,0.0003126133,0.1805395,0.000148765,0.00002137411,0.0001298414,0.003020644,0.0001931381,0.0002288217],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00284609,"threshold_uncertainty_score":0.01429367,"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."}}