{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.005001413,0.0005026938,0.0007540107,0.0005347662,0.0004750974,0.00151463,0.0003585756,0.001039144,0.0007335096],"category_scores_gemma":[0.003712526,0.0003833543,0.0004381107,0.0005626488,0.001096643,0.001648594,0.0009844318,0.00094619,0.0002826454],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003493535,"about_ca_system_score_gemma":0.0003383471,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008607293,"about_ca_topic_score_gemma":0.00256317,"domain_scores_codex":[0.9973918,0.001139033,0.0001386626,0.0005449033,0.0005954627,0.0001901609],"domain_scores_gemma":[0.9971693,0.001201437,0.0007178091,0.0003040215,0.0004456379,0.0001617059],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.001942766,0.0001456973,0.1688851,0.001721047,0.001228168,0.0002955636,0.002292102,0.0003396243,0.6906313,0.0008606598,0.0007570946,0.1309008],"study_design_scores_gemma":[0.00002203519,0.001232176,0.8914123,0.000506848,0.0007623311,0.0006989451,0.004000581,0.0008488244,0.08606941,0.002987047,0.0113495,0.0001100258],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9500005,0.02545225,0.01718652,0.004447512,0.0002184658,0.00002947275,0.0005920938,0.00008842875,0.001984817],"genre_scores_gemma":[0.9597307,0.01573602,0.01759813,0.004703883,0.000218093,0.00005702485,0.0005023504,0.0001461261,0.001307669],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005001413,"threshold_uncertainty_score":0.02645028,"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."}}