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

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 skele...

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Autores principales: 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 C., Lewis, Cecil M., Krause, Johannes, Hofman, Corinne, Bos, Kirsten I., Warinner, Christina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026117/
https://www.ncbi.nlm.nih.gov/pubmed/29959351
http://dx.doi.org/10.1038/s41598-018-28091-9
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author 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 C.
Lewis, Cecil M.
Krause, Johannes
Hofman, Corinne
Bos, Kirsten I.
Warinner, Christina
author_facet 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 C.
Lewis, Cecil M.
Krause, Johannes
Hofman, Corinne
Bos, Kirsten I.
Warinner, Christina
author_sort Mann, Allison E.
collection PubMed
description 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.
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spelling pubmed-60261172018-07-09 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 C. Lewis, Cecil M. Krause, Johannes Hofman, Corinne Bos, Kirsten I. Warinner, Christina Sci Rep Article 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. Nature Publishing Group UK 2018-06-29 /pmc/articles/PMC6026117/ /pubmed/29959351 http://dx.doi.org/10.1038/s41598-018-28091-9 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
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 C.
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
title Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
title_full Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
title_fullStr Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
title_full_unstemmed Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
title_short Differential preservation of endogenous human and microbial DNA in dental calculus and dentin
title_sort differential preservation of endogenous human and microbial dna in dental calculus and dentin
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026117/
https://www.ncbi.nlm.nih.gov/pubmed/29959351
http://dx.doi.org/10.1038/s41598-018-28091-9
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