An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

Francesca J. Standeven; Gwyn Dahlquist-Axe; Jessica Hendy; Sarah Fiddyment; Malin Holst; Krista McGrath; Matthew Collins; Amy Mundorff; Anita Radini; Josef Wagner; Conor J. Meehan; Andrew Tedder; Camilla F. Speller

doi:10.1016/j.dib.2025.111770

An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

Francesca J. Standeven, Gwyn Dahlquist-Axe, Jessica Hendy, Sarah Fiddyment, Malin Holst, Krista McGrath, Matthew Collins, Amy Mundorff, Anita Radini, Josef Wagner, Conor J. Meehan, Andrew Tedder, Camilla F. Speller

Section for Geobiology

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Abstract

Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons' historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR). (c) 2025 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/)

Original language	English
Article number	111770
Journal	Data in Brief
Volume	61
Number of pages	22
ISSN	2352-3409
DOIs	https://doi.org/10.1016/j.dib.2025.111770
Publication status	Published - 2025

Keywords

Ancient DNA
Bioarchaeology
Bioinformatics
Dental calculus
Metagenomics
Oral microbiome

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10.1016/j.dib.2025.111770Licence: CC BY-NC

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Standeven, F. J., Dahlquist-Axe, G., Hendy, J., Fiddyment, S., Holst, M., McGrath, K., Collins, M., Mundorff, A., Radini, A., Wagner, J., Meehan, C. J., Tedder, A., & Speller, C. F. (2025). An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research. Data in Brief, 61, Article 111770. https://doi.org/10.1016/j.dib.2025.111770

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abstract = "Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons' historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR). (c) 2025 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/)",

keywords = "Ancient DNA, Bioarchaeology, Bioinformatics, Dental calculus, Metagenomics, Oral microbiome",

author = "Standeven, {Francesca J.} and Gwyn Dahlquist-Axe and Jessica Hendy and Sarah Fiddyment and Malin Holst and Krista McGrath and Matthew Collins and Amy Mundorff and Anita Radini and Josef Wagner and Meehan, {Conor J.} and Andrew Tedder and Speller, {Camilla F.}",

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AU - Standeven, Francesca J.

AU - Dahlquist-Axe, Gwyn

AU - Hendy, Jessica

AU - Fiddyment, Sarah

AU - Holst, Malin

AU - McGrath, Krista

AU - Collins, Matthew

AU - Mundorff, Amy

AU - Radini, Anita

AU - Wagner, Josef

AU - Meehan, Conor J.

AU - Tedder, Andrew

AU - Speller, Camilla F.

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N2 - Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons' historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR). (c) 2025 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/)

AB - Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons' historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR). (c) 2025 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/)

KW - Ancient DNA

KW - Bioarchaeology

KW - Bioinformatics

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KW - Metagenomics

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