Measuring and mitigating PCR bias in microbiota datasets.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Silverman, JD; Bloom, RJ; Jiang, S; Durand, HK; Dallow, E; Mukherjee, S; David, LA

Published Date

  • July 2021

Published In

Volume / Issue

  • 17 / 7

Start / End Page

  • e1009113 -

PubMed ID

  • 34228723

Pubmed Central ID

  • PMC8284789

Electronic International Standard Serial Number (EISSN)

  • 1553-7358

Digital Object Identifier (DOI)

  • 10.1371/journal.pcbi.1009113


  • eng

Conference Location

  • United States