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Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

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  • Ching Jian
  • Panu Luukkonen
  • Hannele Yki-Järvinen
  • Anne Salonen
  • Katri Korpela

Abstract

The use of relative abundance data from next generation sequencing (NGS) can lead to misinterpretations of microbial community structures, as the increase of one taxon leads to the concurrent decrease of the other(s) in compositional data. Although different DNA- and cell-based methods as well as statistical approaches have been developed to overcome the compositionality problem, and the biological relevance of absolute bacterial abundances has been demonstrated, the human microbiome research has not yet adopted these methods, likely due to feasibility issues. Here, we describe how quantitative PCR (qPCR) done in parallel to NGS library preparation provides an accurate estimation of absolute taxon abundances from NGS data and hence provides an attainable solution to compositionality in high-throughput microbiome analyses. The advantages and potential challenges of the method are also discussed.

Suggested Citation

  • Ching Jian & Panu Luukkonen & Hannele Yki-Järvinen & Anne Salonen & Katri Korpela, 2020. "Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling," PLOS ONE, Public Library of Science, vol. 15(1), pages 1-10, January.
  • Handle: RePEc:plo:pone00:0227285
    DOI: 10.1371/journal.pone.0227285
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    References listed on IDEAS

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    1. James T. Morton & Clarisse Marotz & Alex Washburne & Justin Silverman & Livia S. Zaramela & Anna Edlund & Karsten Zengler & Rob Knight, 2019. "Establishing microbial composition measurement standards with reference frames," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
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    2. Brian D. Williamson & James P. Hughes & Amy D. Willis, 2022. "A multiview model for relative and absolute microbial abundances," Biometrics, The International Biometric Society, vol. 78(3), pages 1181-1194, September.
    3. Koen Wortelboer & Patrick A. Jonge & Torsten P. M. Scheithauer & Ilias Attaye & E. Marleen Kemper & Max Nieuwdorp & Hilde Herrema, 2023. "Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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