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A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus

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The Oral Microbiome

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2327))

Abstract

Ancient dental calculus provides a challenging, yet unparalleled, opportunity to reconstruct ancient oral microbial communities and trace the origins of modern microbiota-associated diseases. Metagenomic analysis of ancient dental calculus using high-throughput DNA sequencing has proven itself as an effective method to accurately reconstruct microorganisms that once lived in the mouths of ancient humans. Here, we provide the strategy, methodologies, and approaches used to establish an ancient dental calculus project, from project conception, community engagement, sampling, extracting DNA, and preparing shotgun metagenomic DNA libraries for sequencing on an Illumina platform. We also discuss techniques to minimize background or contaminant DNA by monitoring and reducing contamination in calculus data sets, utilizing appropriate protective gear, and employing the use of sample decontamination strategies. In this methodology chapter, we hope to promote transparency in the ancient dental calculus research field and encourage collaboration across the ancient DNA research community.

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Authors and Affiliations

  1. Department of Anthropology, The Pennsylvania State University, University Park, PA, USA

    Nicole E. Moore & Laura S. Weyrich

  2. School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia

    Laura S. Weyrich

Authors
  1. Nicole E. Moore
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  2. Laura S. Weyrich
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Corresponding author

Correspondence to Laura S. Weyrich .

Editor information

Editors and Affiliations

  1. College of Dentistry, University of Illinois at Chicago, Chicago, IL, USA

    Guy R. Adami

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Moore, N.E., Weyrich, L.S. (2021). A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus . In: Adami, G.R. (eds) The Oral Microbiome. Methods in Molecular Biology, vol 2327. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1518-8_7

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  • DOI: https://doi.org/10.1007/978-1-0716-1518-8_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1517-1

  • Online ISBN: 978-1-0716-1518-8

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