Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation

Abstract

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500–5000 BP). Inter-individual differences in microbial composition are found to be much larger than intra-individual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.

Ancient dental calculus preserves signatures of biofilm succession and inter-individual variation independent of dental pathology

“…Despite high variability in profiles across teeth within an individual, plaque from any one tooth in an individual is more similar to other teeth in the same individual than to teeth in other individuals (Tamashiro et al, 2021). This pattern of individuality is also captured in ancient dental calculus (Fagernäs et al, 2022), where there is relatively high variability across teeth in an individual, yet samples from one individual are more similar to each other than to samples from another individual.…”

“…Since this pattern of Streptococcus species distribution has now been shown at a continental scale (Fellows Yates et al, 2021b) and within two individual populations (MID, CMB), we next asked whether this pattern holds for an individual, or whether there is intra-individual variation. To investigate tooth-specific Streptococcus species differences with individuals, we used the data published by Fagernäs, et al (Fagernäs et al, 2022). This dataset consists of calculus sampled from 12-18 teeth per individual from 4 individuals.…”

“…Data from Chalcolithic-era dental calculus (ca. 4500–5000 BP) previously reported in Fagernäs, et al (Fagernäs et al, 2022) were included as a comparative dataset to examine intraindividual variation in Streptococcus species. The samples are listed in Supplemental Table S5.…”

“…A similar oral microbial profile at a similar prevalence (11%) was also observed among a diverse range of humans from Europe and Africa from the Paleolithic onwards (Fellows Yates et al, 2021b). Through analysis of the MID assemblage and a set of densely sampled Chalcolithic dentitions (Fagernäs et al, 2022), we demonstrate that this pattern is not associated with dental pathology, but may instead reflect long-term standing variation in patterns of plaque biofilm development among humans.…”

“…Metadata for data processing for published data used in this study are in Supplemental Table S7. The published species table from Supplemental Table S1 in (Fagernäs et al, 2022), was used as input for assessing the distribution of Streptococcus species across the dentition of four individuals. This table was generated by processing the data in a similar manner to the rest of this study.…”