{"doi":"10.1371/journal.pcbi.1009113","title":"Measuring and mitigating PCR bias in microbiota datasets","abstract":"PCR amplification plays an integral role in the measurement of mixed microbial communities via high-throughput DNA sequencing of the 16S ribosomal RNA (rRNA) gene. Yet PCR is also known to introduce multiple forms of bias in 16S rRNA studies. Here we present a paired modeling and experimental approach to characterize and mitigate PCR NPM-bias (PCR bias from non-primer-mismatch sources) in microbiota surveys. We use experimental data from mock bacterial communities to validate our approach and human gut microbiota samples to characterize PCR NPM-bias under real-world conditions. Our results suggest that PCR NPM-bias can skew estimates of microbial relative abundances by a factor of 4 or more, but that this bias can be mitigated using log-ratio linear models.","journal":"PLoS Computational Biology","year":2021,"id":148728,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":120,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9457,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":318527,"name":"Rachael J. Bloom","orcid":"0000-0002-8396-2939","position":1,"is_corresponding":false},{"id":318529,"name":"Sharon Jiang","orcid":"0000-0002-5039-0655","position":2,"is_corresponding":false},{"id":318528,"name":"Heather K. Durand","orcid":"0000-0003-4059-8484","position":3,"is_corresponding":false},{"id":283607,"name":"Eric P. Dallow","orcid":null,"position":4,"is_corresponding":false},{"id":35647,"name":"Sayan Mukherjee","orcid":"0000-0002-6715-3920","position":5,"is_corresponding":false},{"id":44561,"name":"Lawrence A. David","orcid":"0000-0002-3570-4767","position":6,"is_corresponding":false},{"id":249296,"name":"Justin D. Silverman","orcid":"0000-0002-3063-2098","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-18T23:42:46.224799Z","pmid":"34228723","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}