Abstract
Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.
Highlights
Comparing human DNA in dental calculus and dentine, we find that human DNA within dental calculus is generally more fragmented than human DNA in paired dentin samples, with the median length of calculus-derived fragments being approximately 10.3 bp ± 12.0 shorter than that of dentin-derived fragments (Wilcoxon signed-rank test, p = 0.01178); this pattern is largely driven by the relatively long human DNA fragment lengths in dentin, and further work is needed to determine if this is an artifact of sample preparation or a true biological pattern
This higher DNA content of archaeological dental calculus compared to dentin likely reflects biological differences between the two substrates in cellular composition and structure during life, as well as decomposition patterns after death
Dental calculus is formed from dental plaque, a dense microbial biofilm that has been estimated to contain more than 200 million cells per milligram[43]
Summary
Retrieving viable aDNA from archaeological sources, whether from skeletal tissues (bone and dentin) or from secondary substrates (dental calculus and paleofeces), is challenged by post-mortem decomposition, where temporal and environmental factors compromise the molecular stability of DNA. These degradative processes include oxidative and hydrolytic damage to individual bases, hydrolytic lesions on the sugar-phosphate backbone, DNA fragmentation due to nuclease activity, and general degradation by microorganisms involved in the decomposition process[18,19]. We observe a systematic loss of short AT-rich DNA fragments that is marked in bacteria with low to medium GC content genomes
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call