A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

Abstract

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.

Keywords: ancient DNA; dental calculus; metagenomics; metaproteomics; oral microbiome; palaeomicrobiology.

Figure 1.

Early illustration of dental plaque bacteria by Antoni van Leeuwenhoek, 1683/1684. Illustrated bacteria include (A) a rod-shaped motile bacterium, (B) another motile bacterium moving from points (C) to (D), (E) cocci, (F) fusiform bacteria and (G) a spirochaete. Adapted from [57].

Figure 2.

Backscattered scanning electron microscopy image of archaeological dental calculus in situ on the labial surface of a mandibular incisor. (a) Dental pulp cavity; (b) taphonomically altered dentine; (c) intact dentine; (d) enamel; (e) detail of dental calculus mineral layers and an in situ microfossil inclusion of biogenic silica (arrow); (f) detail of oral bacteria within dental calculus. The specimen shown is from Dalheim, Germany, and has been radiocarbon dated to 1079 ± 51 CE (calibrated) [39].