Dental Calculus: Using Oral Microbiota to Understand Pathogens

Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we, therefore, lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient diseases and how archaeological studies can contribute to a medical understanding of health and nutrition today.

Upon death, the ecology of the human microbiome transforms dramatically through the process of soft tissue decomposition (Morris et al., 2006). With the exception of frozen and mummified remains, only two microbiomes routinely produce substrates that, under favorable conditions, persist after death in archaeological contexts: fecal material of the gut microbiome may desiccate or mineralize to produce coprolites, and dental plaque of the oral microbiome calcifies in situ during life such that by the time of death it is already in a semi-fossilized state known as dental calculus that resists decomposition and thus continues to preserve after death. The opportunity to investigate ancient microbiomes directly through coprolites and dental calculus allow us to redefine questions of past human health within a much broader framework that includes not only the investigation of pathogens but also the carriage rates and risks posed by endemic and dormant pathogens, as well as the health and resiliency of the overall microbial community. Finally, in the case of dental calculus, it may even be possible to reconstruct a life history of the disease, including the survivorship of past pandemics.

Adler et al. (2017) performed the first NGS analysis of ancient dental calculus and demonstrated that dental calculus could be used to characterize ancient oral microbiomes. Amplifying the 16S rRNA gene third hypervariable region (V3), they performed phylum-level comparisons of dental calculus bacteria in Mesolithic, Neolithic, Bronze Age, medieval and modern samples, and reported ecological shifts in members of the oral microbiome corresponding to the origins of agriculture and the Industrial Revolution. Subsequently, Warinner (2018a) used shotgun metagenomic and metaproteomic approaches, in combination with 16S rRNA gene sequencing, to reconstruct a species-level taxonomic and protein functional characterization of medieval dental calculus samples. Their study revealed that the oral microbiome has long served as a reservoir for a diverse range of opportunistic pathogens and low-level antibiotic resistance genes. From these data, they were able to characterize active periodontal disease based on evidence of bacterial virulence factors and host immune activity, and reconstruct the genome of the periodontal pathogen, Tannerella forsythia!

Considering the near-ubiquity of dental calculus in the archaeological records, these studies provide a first glimpse at the potential wealth of evolutionary and health information that ancient oral microbiome research is likely to provide as more geographically and temporally diverse populations are investigated.