{"id":"W3184787924","doi":"10.3390/vetsci8070138","title":"Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories","year":2021,"lang":"en","type":"article","venue":"Veterinary Sciences","topic":"Ruminant Nutrition and Digestive Physiology","field":"Agricultural and Biological Sciences","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan; University of Alberta","funders":"Alberta Livestock and Meat Agency","keywords":"Biology; Shotgun sequencing; Bacteroidetes; Firmicutes; Microbiome; Metagenomics; Rumen; Pyrosequencing; Amplicon sequencing; Amplicon; Proteobacteria; Deep sequencing; Shotgun; Phylum; Lactococcus; DNA sequencing; 16S ribosomal RNA; Genetics; Food science; Bacteria; Gene; Polymerase chain reaction; Genome","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":[0.0003123136,0.0002103404,0.0002426647,0.00002052923,0.0009795952,0.0002184386,0.0004411409,0.00005858974,0.0002179276],"category_scores_gemma":[0.0001115455,0.00006207656,0.0001181773,0.0004447641,0.0003847116,0.00017476,0.0002552521,0.0001385466,0.0000174218],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004972352,"about_ca_system_score_gemma":0.00001565486,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003338717,"about_ca_topic_score_gemma":0.00001597288,"domain_scores_codex":[0.9980056,0.0007506489,0.0001812691,0.0004851596,0.0001983261,0.0003790459],"domain_scores_gemma":[0.9980307,0.001668626,0.00008714372,0.00009100841,0.0000411519,0.0000813291],"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":[0.00002029507,0.0000727279,0.001335215,0.00001384755,0.000007042276,0.00002433586,0.0000954425,0.000001269452,0.9661995,0.0002386113,0.0001621124,0.03182963],"study_design_scores_gemma":[0.0001199508,0.002583875,0.420004,0.0001827698,0.00001331837,0.00007668953,0.001493041,0.00009657663,0.5658745,0.00230706,0.00689918,0.0003490562],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9937674,0.0005346792,0.00001169113,0.004049808,0.0005694474,0.000139625,0.00001286967,0.00005348957,0.0008609813],"genre_scores_gemma":[0.9981622,0.0001122161,0.0003831926,0.0009241097,0.0001938677,0.00002428703,0.00001715743,0.000001031498,0.0001819473],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4186688,"threshold_uncertainty_score":0.7534353,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1275837021137153,"score_gpt":0.3397306417963329,"score_spread":0.2121469396826176,"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."}}