TY - UNPB

T1 - Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus

AU - Bartholdy, Bjørn Peare

AU - Velsko, Irina M.

AU - Gur-Arieh, Shira

AU - Fagernäs, Zandra

AU - Warinner, Christina

AU - Henry, Amanda G.

PY - 2023

Y1 - 2023

N2 - Dental calculus is increasingly used by researchers to study dietary patterns in past populations. Thebenefits of using dental calculus for this purpose have been clearly demonstrated in previous studies,with dental calculus harbouring a wealth of microremains and biomarkers for health and diet withinits mineral matrix. Previous studies have demonstrated some of the limitations and biases of howmethods of processing may overlook, or even remove, some of the important information containedwithin the mineralised matrix. However, there are many factors that are impossible to account forin vivo and in archaeological material, such as exact dietary intake, and individual factors such aspH and enzyme activity, leaving some limitations that may not be addressed through these types ofstudies and will require a different approach.We present a protocol for creating a calcifying oral biofilm model that can be used to explore thebiases and limitations of dental calculus as a medium for paleodietary reconstructions. We report themicrobial and mineral composition of our model in an effort to validate the model calculus as an ap-propriate proxy to natural dental calculus. The microbial profile and species diversity of our modelwas determined using metagenomic classification with the nf-core/eager pipeline and Kraken2, andcompared to various reference samples from oral sites, including saliva, plaque, and dental calculus.We then assessed whether our model calculus mineralises in a manner similar to natural dental calcu-lus using Fourier transform infrared (FTIR) spectroscopy. The metagenomic classification showed amicrobial profile predominantly made up of (facultative) anaerobes, with a community structure thatwas somewhat distinct from other oral reference samples. The core genera of the model consistedof oral species, but clustered separately from oral reference samples, with a higher abundance ofanaerobes.Mineral and organic components of our model mimic that of the modern and archaeological ref-erence calculus that was used as a comparison. There was an overall increase in the inorganiccomponent relative to organic over the course of the experiment, with carbonated hydroxyapatite asthe principal compound, consistent with natural human-derived calculus.We conclude that oral biofilm models, such as the one presented in this study, have great potential tovalidate current methods used in the analysis of archaeological dental calculus, and should be usedto complement, rather than replace current in vivo studies.

AB - Dental calculus is increasingly used by researchers to study dietary patterns in past populations. Thebenefits of using dental calculus for this purpose have been clearly demonstrated in previous studies,with dental calculus harbouring a wealth of microremains and biomarkers for health and diet withinits mineral matrix. Previous studies have demonstrated some of the limitations and biases of howmethods of processing may overlook, or even remove, some of the important information containedwithin the mineralised matrix. However, there are many factors that are impossible to account forin vivo and in archaeological material, such as exact dietary intake, and individual factors such aspH and enzyme activity, leaving some limitations that may not be addressed through these types ofstudies and will require a different approach.We present a protocol for creating a calcifying oral biofilm model that can be used to explore thebiases and limitations of dental calculus as a medium for paleodietary reconstructions. We report themicrobial and mineral composition of our model in an effort to validate the model calculus as an ap-propriate proxy to natural dental calculus. The microbial profile and species diversity of our modelwas determined using metagenomic classification with the nf-core/eager pipeline and Kraken2, andcompared to various reference samples from oral sites, including saliva, plaque, and dental calculus.We then assessed whether our model calculus mineralises in a manner similar to natural dental calcu-lus using Fourier transform infrared (FTIR) spectroscopy. The metagenomic classification showed amicrobial profile predominantly made up of (facultative) anaerobes, with a community structure thatwas somewhat distinct from other oral reference samples. The core genera of the model consistedof oral species, but clustered separately from oral reference samples, with a higher abundance ofanaerobes.Mineral and organic components of our model mimic that of the modern and archaeological ref-erence calculus that was used as a comparison. There was an overall increase in the inorganiccomponent relative to organic over the course of the experiment, with carbonated hydroxyapatite asthe principal compound, consistent with natural human-derived calculus.We conclude that oral biofilm models, such as the one presented in this study, have great potential tovalidate current methods used in the analysis of archaeological dental calculus, and should be usedto complement, rather than replace current in vivo studies.

U2 - 10.1101/2023.05.23.541904

DO - 10.1101/2023.05.23.541904

M3 - Preprint

BT - Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus

PB - bioRxiv

ER -