Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool

Rita M Austin; Tanvi P Honap; Allison E Mann; Alexander Hübner; Cassandra M S DeGaglia; Christina Warinner; Molly K Zuckerman; Courtney A Hofman

doi:10.1038/s41598-024-64818-7

Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool

Sci Rep. 2024 Jun 26;14(1):14720. doi: 10.1038/s41598-024-64818-7.

Authors

Rita M Austin^{1

2

3

4}, Tanvi P Honap^{5

6}, Allison E Mann⁷, Alexander Hübner⁸, Cassandra M S DeGaglia⁹, Christina Warinner¹⁰, Molly K Zuckerman¹¹, Courtney A Hofman^{12

13

14}

Affiliations

¹ Frontiers in Evolutionary Zoology Research Group, Natural History Museum of Oslo, University of Oslo, Oslo, 0562, Norway. [email protected].
² Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA. [email protected].
³ Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA. [email protected].
⁴ Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA. [email protected].
⁵ Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
⁶ Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA.
⁷ Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA.
⁸ Department Archaeogenetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
⁹ Department of Anthropology, Tulane University, New Orleans, LA, 70118, USA.
¹⁰ Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA.
¹¹ Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS, 39762, USA. [email protected].
¹² Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA. [email protected].
¹³ Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA. [email protected].
¹⁴ Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA. [email protected].

Abstract

Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution's Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp. pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.

Keywords: Ancient DNA; Dental calculus; Interdisciplinary; Pathogen identification; Robert J. Terry Collection; Tuberculosis.

Publication types

Historical Article

MeSH terms

Adult
DNA, Bacterial / genetics
Dental Calculus* / history
Dental Calculus* / microbiology
Female
Humans
Male
Metagenome / genetics
Metagenomics* / methods
Middle Aged
Mycobacterium tuberculosis* / genetics
Mycobacterium tuberculosis* / isolation & purification
Paleopathology* / methods
Syphilis / diagnosis
Syphilis / history
Syphilis / microbiology
Treponema pallidum / genetics
Treponema pallidum / isolation & purification
Tuberculosis* / diagnosis
Tuberculosis* / microbiology

Substances

DNA, Bacterial

Abstract

Publication types

MeSH terms

Substances

Grants and funding