{"id":"W4411497601","doi":"10.1038/s41564-025-02035-2","title":"Guidelines for preventing and reporting contamination in low-biomass microbiome studies","year":2025,"lang":"en","type":"review","venue":"Nature Microbiology","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":79,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Guelph","funders":"Department of Microbiology, Faculty of Science, Chulalongkorn University; Monash Biomedicine Discovery Institute, Monash University; School of Life and Environmental Sciences, Deakin University; National Health and Medical Research Council; Australian Research Council; Irving Medical Center, Columbia University; Huck Institutes of the Life Sciences; Centre for Biotechnology and Bioengineering; VetAgro Sup; Ludwig-Maximilians-Universität München; Japan Agency for Marine-Earth Science and Technology; Genome Institute of Singapore; Colorado State University; Universiteit Stellenbosch; University of Melbourne; Monash University; University of Sydney; University of California, San Diego; University of New South Wales; Centre National de la Recherche Scientifique; Cooperative Institute for Research in Environmental Sciences; University of Colorado Boulder; National Science Foundation; University of Aberdeen; College of Veterinary Medicine, North Carolina State University; Department of Education and Training; Office of Polar Programs; University of Washington; Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement; Agency for Science, Technology and Research; Human Frontier Science Program; North Carolina State University; Universidad de Antofagasta; National University of Singapore","keywords":"Contamination; Biomass (ecology); Metagenomics; Microbiome; Environmental science; Biotechnology; Environmental chemistry; Biology; Ecology; Bioinformatics; Chemistry","routes":{"ca_aff":true,"ca_fund":false,"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":["metaepi_narrow","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.001326513,0.0005008894,0.00185663,0.0003522384,0.0001162992,0.00002052782,0.0002450826,0.002065549,0.00000169579],"category_scores_gemma":[0.002918324,0.0004197728,0.0003559988,0.0002353205,0.0001189535,0.000003506713,0.0003253955,0.0005048097,0.000001323226],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009420019,"about_ca_system_score_gemma":0.0004310852,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006576159,"about_ca_topic_score_gemma":0.0001722643,"domain_scores_codex":[0.9962911,0.0002059565,0.002014336,0.000972578,0.00002362297,0.0004924308],"domain_scores_gemma":[0.9972186,0.0001602034,0.001739444,0.0003406113,0.0005033009,0.00003785213],"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":[0.00005895836,0.0001090125,0.0001026774,0.1292177,0.0008454557,0.00002010772,0.00007709423,3.231959e-7,0.4245232,0.0001078232,0.03259507,0.4123425],"study_design_scores_gemma":[0.0005008755,0.00009740669,0.00001126959,0.01148155,0.0002255906,0.0002550855,0.00003978901,3.153279e-7,0.002267326,0.0000233401,0.9847037,0.000393756],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.001603714,0.9954072,0.00005228368,0.0001915305,0.0008313855,0.001588296,0.0002812769,0.0000155469,0.00002872772],"genre_scores_gemma":[0.0001316757,0.9918439,0.002131122,0.0004931016,0.000340458,0.0001638567,0.003207901,0.00004247197,0.001645476],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9521086,"threshold_uncertainty_score":0.9998254,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07399262734990877,"score_gpt":0.4581998956544402,"score_spread":0.3842072683045314,"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."}}