What would happen if the richest depository of an old individual was right there in front of our very eyes, incinerated in a tooth?
Calcified plaque or archaeological dental calculus has ceased to pose a source of inconvenience to the curators and has become a highly sought after substrate in molecular science. By comparison in 48 different individuals, dental calculus shotgun sequenced revealed significantly greater yields of total DNA than dentin, although both may be in the same tooth. The abundance can be important since ancient biomolecules are usually obtained in degraded fragments in the presence of environmental contaminants, and the sequencing scale can often be the difference between a signal and noisy background.
Calculus advantage is mechanical rather than molecular. Plaque starts as a thick biofilm as a trap of microbial cells, host debris, and food and environmental particles; the mixture is then fixed when mineralized into a crystalline framework. That same study also attributes the performance of calculus to rapid formation of calcium phosphate minerals which bind DNA to form a structure termed as comparatively inert and more difficult to be penetrated by the microbes. Dentin, however, is mostly acellular in vivo, and when dead it is as a rule a canvas to soil and manipulating microbes. The outcome is inversion of the methodology: the part of the body which appears to be “cleaner” anatomically is often more messy genetically.
The messiness is reflected in microbial profiles. Calculus samples in the paired dataset were tightly clustered by community composition seen as a preserved oral microbiome, and dentin samples were diverse and were biased towards environmental taxa. Estimates of source-tracking in the same work gave peak skin and soil contributions in calculus of 7.9 and 14.0%, compared to 33.5% and89.0% in dentin. The pragmatic consequence is not merely to have “more DNA,” but to have more interpretable DNA: calculus is more likely to have an organized biological community than a collage of post-burial colonizers.
The paradox of calculus is human DNA. The contribution of the host is minimal and consistent: mean 0.08% of reads (range 0.007 0.47) in calculus and the mean of dentin is extremely variable, with a mean of 13.70% (range 0.00370.14%). Calculus-derived human fragments are also reported to be regularly shorter in the same analysis (on average approximately 10.3 bp shorter than paired dentin human fragments) indicating that calculus is not a human tissue reservoir but rather a molecular trap.
Mechanism influences the survival. The paper talks about the entry of host DNA into calculus by: shed cells; inflammatory processes such as neutrophil-to-neutrophil communication by extracellular neutrophile traps via neutrophil extracellular chromatin decondensation (NETosis). Uncovered DNA in such an environment is susceptible to nucleases that are produced by oral flora, which can be used to explain why host DNA in calculus is usually highly fragmented despite the relative intactness of microbial DNA.
Clues which run beyond ancestry are also retained by calculus. In Japan in the Edo period, dietary and lifestyle taxa were studied by applying DNA metabarcoding to dental calculus of 13 individuals, with Oryza sequences being detected in most of the samples by genus-specific PCR and a variety of plant and fungal groups were recovered by barcode sequencing. The illustration of the importance of targeted approaches is that in calculus, most of the DNA is of microbial origin, and, therefore, short amplicons and strong precautions are the distinction between obtainable signals and run-to-run carryover.
In these works, the “gold rush” is not about a single spectacle genome as it is about a reproducible substrate that encodes the microbiomes, trace host DNA, and environmental signatures in a single mineralized film. Dental calculus is not a substitute of high yield human genomics of petrous bone or tooth cementum, but it alters what we can ask of large collections: how the oral ecosystem changed with diet, hygiene, and disease, and how minute, damaged fragments of host DNA can nonetheless be authenticated, enriched, and read as a larger molecular biography.
