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

Abstract

Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed inter-individual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.Research HighlightsNo associations between calculus species profiles and oral health metrics were detected in a single large populationA minority of individuals have a dental calculus species profile characterized by low levels of Streptococcus and high levels of anaerobic taxa

Exploring archaeogenetic studies of dental calculus to shed light on past human migrations in Oceania

“…However, the extent to which loss of AT-rich fragments affects species profiles, perhaps skewing older samples to have higher proportions of high-GC taxa, has not yet been extensively explored. We found that the species with the strongest PC1 loadings (Supplemental Table S3) suggested a taxonomic gradient relating to oxygen tolerance, such as that previously described in calculus samples from the archaeological site of Middenbeemster in the Netherlands 15 , but there was no clear association with GC content.…”

“…When controlling for the lab in which samples were processed, island (R 2 = 0.2045, F = 1.650, p = 0.035) and average GC content (R 2 = 0.0761, F = 7.372, p = 0.01) were still significant drivers of the sample community composition. The average GC content of calculus is known to increase with sample age 11,14,15 through the taphonomic loss of AT-rich DNA fragments, and most islands are represented by samples from a single time period, therefore tying island and age/GC content.…”

“…A second comparative dataset was used to compare calculus species profiles across the globe, and consisted of ancient calculus samples from 6 previously published studies. These included samples from Japan 16 , Europe and Africa 10 , Europe 15,18,24 , and Europe, the Caribbean, North America, and Mongolia 11 (Supplemental Table S2).…”

“…Missing data for some islands was obtained from alternative sources 58,59 . Preservation of microbial DNA in calculus and of human DNA in bone samples was compared in the Pacific and in Europe using previously published datasets 1,5,15,24,60,61 . For details see Supplemental Methods.…”

“…Preservation was investigated and visualized using SourceTracker v.1.01 15 . A species-level OTU table was used as input, and the reference metagenomic datasets described in the main text were used as sources.…”