{"id":"W4405073788","doi":"10.1128/aem.01759-24","title":"Transcriptional delineation of polysaccharide utilization loci in the human gut commensal <i>Segatella copri</i> DSM18205 and co-culture with exemplar <i>Bacteroides</i> species on dietary plant glycans","year":2024,"lang":"en","type":"article","venue":"Applied and Environmental Microbiology","topic":"Microbial Metabolites in Food Biotechnology","field":"Nursing","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Glycan; Bacteroides; Biology; Bacteroides thetaiotaomicron; Polysaccharide; Microbiome; Microbiology; Computational biology; Commensalism; Transcriptome; Gut microbiome; Genetics; Evolutionary biology; Bacteria; Gene; Biochemistry; Gene expression; Glycoprotein","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":[0.000126655,0.0002209732,0.0002503266,0.00009816568,0.0001211369,0.00002452248,0.0001241523,0.0002446823,0.00003137856],"category_scores_gemma":[0.000001501353,0.0001537934,0.00002841757,0.00008498841,0.0006493808,0.00004331373,0.00003170226,0.0003261847,0.000005136732],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004783832,"about_ca_system_score_gemma":0.000003730507,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002683084,"about_ca_topic_score_gemma":0.0000476329,"domain_scores_codex":[0.9990008,0.00006826407,0.0002806862,0.0003690023,0.00005864473,0.0002225703],"domain_scores_gemma":[0.9997038,0.00005920055,0.00006245785,0.0001486182,0.000002459154,0.00002351868],"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":[0.0002618159,0.000100037,0.001156323,0.00004797294,0.00003265567,0.000005473916,0.001265534,0.00000926625,0.9932706,0.00158124,0.000614129,0.001654949],"study_design_scores_gemma":[0.001670769,0.001036835,0.01101316,0.0001015357,0.0001318743,0.0005117452,0.002006237,0.00004013321,0.8966473,0.0003524843,0.08607762,0.0004102456],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9962994,0.001506371,0.0000756886,0.0007124331,0.00009471043,0.000361937,0.0007935135,0.00003124681,0.0001247359],"genre_scores_gemma":[0.9963998,0.000469629,0.0001443093,0.001266354,0.00005418456,0.00001371999,0.001611365,0.00001999917,0.00002060562],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09662324,"threshold_uncertainty_score":0.6271514,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01851434947864789,"score_gpt":0.2306715343906514,"score_spread":0.2121571849120035,"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."}}