Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes
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Abstract
Previous research has reported effects of sample storage conditions and DNA isolation procedures on metagenomics-based microbiome composition; however, the effect of library preparation and DNA sequencing in metagenomics has not been thoroughly assessed. Here, we provide evidence that library preparation and sequencing platform introduce systematic biases in the metagenomic-based characterization of microbial communities.
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Bias can be introduced throughout all stages of sample processing, including selection of sample collection protocol, preservative choice, storage temperature, DNA extraction protocol, library preparation, sequencing platform, and bioinformatics analysis pipeline.
“Bias can be introduced throughout all stages of sample processing, including the selection of sample collection protocol, preservative choice, storage temperature, DNA extraction protocol, library preparation, sequencing platform, and bioinformatics analysis pipeline.720–723”
From Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases (2024) · cites this paper as [723]
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- Authors
- Poulsen, C. S., Ekstrøm, C. T., Aarestrup, F. M., & Pamp, S. J.
- Affiliations
- Technical University of Denmark (DK)
- University of Copenhagen (DK)
- Novo Nordisk Foundation (DK)
- Corresponding author
- Pamp, Sünje J.
- Venue
- Microbiology Spectrum
- Publisher
- American Society for Microbiology
- Published
- 2022-04-27
- Volume
- 10
- Issue
- 2
- Pages
- e0009022-e0009022
- ISSN
- 2165-0497 (ISSN-L)
- PMC
- PMC9045301
- OpenAlex
- W4220737584
- Cited by
- 50
- References
- 51
- Citations by year
- 2026: 12 · 2025: 9 · 2024: 11 · 2023: 10 · 2022: 2 · 2021: 3 · 2020: 3
- FWCI
- 0.83
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Microbiology Spectrum (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Funders
- Horizon2020 (643476)
- Novo Nordisk Foundation (NNF16OC0021856)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- metagenomics, microbiome, library preparation bias, systematic bias, microbial community composition, sample metadata, DNA sequencing
- MeSH terms
- Animals, Bacteria, DNA, Swine, Bias, Sequence Analysis, DNA, Metagenomics, High-Throughput Nucleotide Sequencing, Microbiota
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