Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling
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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.
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If the compositional property is not accounted for, the likelihood of introducing false positives in differential abundance analysis and negative correlation biases in correlation-based analysis increases heavily.
“If this statistical property is not accounted for, the likelihood of introducing false positives in differential abundance analysis59,60 and negative correlation biases in correlation-based analysis61,62 increases heavily.”
From Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma (2024) · cites this paper as [61]
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- Authors
- Jian, C., Luukkonen, P., Yki-Järvinen, H., Salonen, A., & Korpela, K.
- Affiliations
- University of Helsinki (FI)
- Corresponding author
- Korpela, Katri
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2020-01-15
- Volume
- 15
- Issue
- 1
- Pages
- e0227285
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC6961887
- OpenAlex
- W3000731297
- Cited by
- 384
- References
- 35
- Citations by year
- 2026: 37 · 2025: 58 · 2024: 55 · 2023: 61 · 2022: 59 · 2021: 63 · 2020: 44 · 2019: 7
- FWCI
- 18.39
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Työväentutkimus Vuosikirja (submittedVersion)
- Funders
- Helsingin Yliopisto
- the EU/EFPIA Innovative Medicines Initiative Joint Undertaking (115372)
- Horizon 2020 Framework Programme (634413)
- Academy of Finland
- Otto A. Malm Lahjoitusrahasto
- Sigrid Juséliuksen Säätiö
- EVO
- Finnish Medical
- Alfred Kordelinin Säätiö
- Paulon Säätiö
- Jalmari and Rauha Ahokas and Novo Nordisk
- Mary and Georg C. Ehnrooth
- Biocodex Microbiota foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- real-time PCR, microbiota profiling, compositional data, human microbiome, NGS library preparation, microbial community structure
- MeSH terms
- Bacteria, DNA, Bacterial, Feasibility Studies, Humans, RNA, Ribosomal, 16S, Gene Library, Randomized Controlled Trials as Topic, High-Throughput Screening Assays, High-Throughput Nucleotide Sequencing, Real-Time Polymerase Chain Reaction, Microbiota
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