Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.
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Authors
Ziesemer, Kirsten A
Mann, Allison E
Sankaranarayanan, Krithivasan
Schroeder, Hannes
Ozga, Andrew T
Brandt, Bernd W
Zaura, Egija
Waters-Rist, Andrea
Hoogland, Menno
Salazar-García, Domingo C
Aldenderfer, Mark
Speller, Camilla
Hendy, Jessica
Weston, Darlene A
MacDonald, Sandy J
Thomas, Gavin H
Collins, Matthew J
Lewis, Cecil M
Hofman, Corinne
Warinner, Christina
Publication Date
2015-11-13Journal Title
Sci Rep
ISSN
2045-2322
Publisher
Springer Science and Business Media LLC
Volume
5
Pages
16498
Language
eng
Type
Article
Physical Medium
Electronic
Metadata
Show full item recordCitation
Ziesemer, K. A., Mann, A. E., Sankaranarayanan, K., Schroeder, H., Ozga, A. T., Brandt, B. W., Zaura, E., et al. (2015). Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.. Sci Rep, 5 16498. https://doi.org/10.1038/srep16498
Abstract
To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.
Keywords
Dental Calculus, Humans, Bacteria, Methanobrevibacter, RNA, Ribosomal, 16S, Phylogeny, Gene Amplification, Nucleic Acid Conformation, Archaeology, Female, Male, Metagenome, Metagenomics, High-Throughput Nucleotide Sequencing, Microbiota, Gastrointestinal Microbiome
Identifiers
External DOI: https://doi.org/10.1038/srep16498
This record's URL: https://www.repository.cam.ac.uk/handle/1810/285854
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