ArticlePLoS computational biology2021
Measuring and mitigating PCR bias in microbiota datasets.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.PloS one · 2021Trial
- Accounting for Variability Across Years, Depths, and Non-Target Reads Improves Quantification of Root Community Composition in Plant Mixtures.Molecular ecology resources · 2026Article
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
- MATRIX: rapid quantification of total and active microbial cells with single-cell phenotypes for environmental microbiomes.mSystems · 2026Article
- NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.BMC bioinformatics · 2026Article
- From soil to sequences: mechanisms and tools unravelling plant-rhizomicrobiome interactions.World journal of microbiology & biotechnology · 2026Review
- The Evolution of Bees: Insights from 'Omic Studies.Genome biology and evolution · 2026Review
- The longitudinal expression ofMicrobiology (Reading, England) · 2026Article
- Biological and technical variability in mouse microbiota analysis and implications for sample size determination.Lab animal · 2026Article
- PCR bias impacts microbiome ecological analyses.PLoS computational biology · 2026Article
- Optimized protocol for profiling mucosa-associated microbiota from formalin-fixed paraffin-embedded gut tissues from treatment-naïve pediatric patients with Crohn's disease.Frontiers in cellular and infection microbiology · 2026Article
- Evaluating Prey Availability for the Rice's Whale (Ecology and evolution · 2026Article
- mbSparse: an autoencoder-based imputation method to address sparsity in microbiome data.Gut microbes · 2025Article
- A Comprehensive Review: Molecular Diagnostics and Multi-Omics Approaches to Understanding Bovine Respiratory Disease.Veterinary sciences · 2025Review
- Predicting sequence-specific amplification efficiency in multi-template PCR with deep learning.Nature communications · 2025Article
- Observation Bias in Metabarcoding.Molecular ecology resources · 2025Article
- Metagenomic analysis of pathogenicity of puccinia xanthii on invasive plant xanthium italicum.Scientific reports · 2025Article
- How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads.Quantitative biology (Beijing, China) · 2025Review
- PCR Bias Impacts Microbiome Ecological Analyses.bioRxiv : the preprint server for biology · 2025Article
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7 authors.
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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.
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