Title

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

Authors

Kirsten Ziesemer, Leiden University
Allison Mann, University of Oklahoma
Krithivasan Sankaranarayanan, University of Oklahoma
Hannes Schroeder, Leiden University; University of Copenhagen
Andrew T. Ozga, University of OklahomaFollow
Bernd W. Brandt, University of Amsterdam and VU University Amsterdam
Egija Zaura, University of Amsterdam and VU University Amsterdam
Andrea Waters-Rist, Leiden University
Menno Hoogland, Leiden University
Domingo C. Salazar-Garcia, University of Cape Town; Universitat de València; Max-Planck Institute for Evolutionary Anthropology
Mark Aldenderfer, University of California, Merced
Camilla Speller, University of York
Jessica Hendy, University of York
Darlene A. Weston, Leiden University; University of British Columbia
Sandy J. MacDonald, University of York
Gavin H. Thomas, University of York
Matthew J. Collins, University of York
Cecil M. Lewis Jr., University of Oklahoma
Corinne Hofman, Leiden University
Christina Warinner, University of Oklahoma

Document Type

Article

Publication Date

11-13-2015

Publication Title

Scientific Reports

Keywords

Environmental microbiology, Microbial ecology, Microbial genetics

ISSN

2045-2322

Volume

5

Issue/No.

16498

First Page

1

Last Page

19

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. coli341–534) 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 silicoanalysis 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.

Comments

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NSUWorks Citation

Ziesemer, Kirsten; Allison Mann; Krithivasan Sankaranarayanan; Hannes Schroeder; Andrew T. Ozga; Bernd W. Brandt; Egija Zaura; Andrea Waters-Rist; Menno Hoogland; Domingo C. Salazar-Garcia; Mark Aldenderfer; Camilla Speller; Jessica Hendy; Darlene A. Weston; Sandy J. MacDonald; Gavin H. Thomas; Matthew J. Collins; Cecil M. Lewis Jr.; Corinne Hofman; and Christina Warinner. 2015. "Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification." Scientific Reports 5, (16498): 1-19. doi:10.1038/srep16498.

ORCID ID

0000-0003-4540-7106

ResearcherID

D-1147-2018

DOI

10.1038/srep16498