Differential preservation of endogenous human and microbial DNA in dental calculus and dentin

Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Åshild J. Vågene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-García, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne Stone, Cecil M. Lewis, Johannes Krause, Corinne Hofman, Kirsten I. BosChristina Warinner

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007-0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003-70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.

Original languageEnglish (US)
Article number9822
JournalScientific Reports
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2018

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Dental Calculus
Dentin
DNA
Microbiota
Metagenomics
Dental Plaque
Base Composition
Firearms
DNA Fragmentation
Cellular Structures

ASJC Scopus subject areas

  • General

Cite this

Mann, A. E., Sabin, S., Ziesemer, K., Vågene, Å. J., Schroeder, H., Ozga, A. T., ... Warinner, C. (2018). Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports, 8(1), [9822]. https://doi.org/10.1038/s41598-018-28091-9

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. / Mann, Allison E.; Sabin, Susanna; Ziesemer, Kirsten; Vågene, Åshild J.; Schroeder, Hannes; Ozga, Andrew T.; Sankaranarayanan, Krithivasan; Hofman, Courtney A.; Fellows Yates, James A.; Salazar-García, Domingo C.; Frohlich, Bruno; Aldenderfer, Mark; Hoogland, Menno; Read, Christopher; Milner, George R.; Stone, Anne; Lewis, Cecil M.; Krause, Johannes; Hofman, Corinne; Bos, Kirsten I.; Warinner, Christina.

In: Scientific Reports, Vol. 8, No. 1, 9822, 01.12.2018.

Research output: Contribution to journalArticle

Mann, AE, Sabin, S, Ziesemer, K, Vågene, ÅJ, Schroeder, H, Ozga, AT, Sankaranarayanan, K, Hofman, CA, Fellows Yates, JA, Salazar-García, DC, Frohlich, B, Aldenderfer, M, Hoogland, M, Read, C, Milner, GR, Stone, A, Lewis, CM, Krause, J, Hofman, C, Bos, KI & Warinner, C 2018, 'Differential preservation of endogenous human and microbial DNA in dental calculus and dentin', Scientific Reports, vol. 8, no. 1, 9822. https://doi.org/10.1038/s41598-018-28091-9
Mann, Allison E. ; Sabin, Susanna ; Ziesemer, Kirsten ; Vågene, Åshild J. ; Schroeder, Hannes ; Ozga, Andrew T. ; Sankaranarayanan, Krithivasan ; Hofman, Courtney A. ; Fellows Yates, James A. ; Salazar-García, Domingo C. ; Frohlich, Bruno ; Aldenderfer, Mark ; Hoogland, Menno ; Read, Christopher ; Milner, George R. ; Stone, Anne ; Lewis, Cecil M. ; Krause, Johannes ; Hofman, Corinne ; Bos, Kirsten I. ; Warinner, Christina. / Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. In: Scientific Reports. 2018 ; Vol. 8, No. 1.
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