The dental calculus metabolome in modern and historic samples

Irina M Velsko,Krithivasan Sankaranarayanan,Laurent A F Frantz,Joshua J Coon,Louise Loe,Juan Bautista Rodriguez Martinez,Greger Larson,Lauren Klaus,Katherine A Overmyer,Eros Chaves,Matthew J Collins,Christina Warinner,Camilla Speller,Cecil M Lewis

doi:10.1007/s11306-017-1270-3

Abstract

IntroductionDental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens.ObjectiveWe present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach.MethodsUltra performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography–MS (GC–MS) and UPLC–MS/MS for further characterization of metabolites and lipids. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss.ResultsDipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples.ConclusionsThe results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.

Highlights

Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts
A total of 285 metabolites were identified by ultra-performance liquid chromatography (UPLC)–MS/ MS in the 17 dental calculus samples, and these were categorized as members of one of eight super-groups: Amino acids, Carbohydrates, Cofactors and vitamins, Energy, Lipids, Nucleotides, Peptides, and Xenobiotics (Fig. 1a; Supplemental Table S1), which were further classified into 69 sub-categories
A smaller subset of historic calculus was analyzed by gas chromatography–MS (GC–MS) and LC–MS at the University of Wisconsin-Madison; this enabled the identification of 15 additional metabolites and 40 additional lipids, respectively (Fig. 1b; Table S2)

Summary

Introduction

Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Obtained human biofluids including serum (Psychogios et al 2011), urine (Bouatra et al 2013), and saliva (Dame et al 2015) have been extensively profiled to define the range of metabolites that are produced in health, and how their levels fluctuate based on changes in activity (Daskalaki et al 2015), diet (Lankinen et al 2014), drug use (Fleet et al 2008; Hahn et al 1972), and disease progression (Yan et al 2008) These studies have made it possible to search for specific metabolites that can act as biomarkers for a diverse range of disorders and diseases, including cardiovascular disease (Jensen et al 2014), diabetes (Sysi-Aho et al 2011), periodontal disease (Barnes et al 2009, 2011), and cancer (Beger 2013). Because of the presence of serum-derived molecules, saliva has been used to search for biomarkers both of local diseases, such as periodontal disease (Barnes et al 2011) and oral cancer (Yan et al 2008), and systemic diseases such as pancreatic and breast cancers (Sugimoto et al 2010), and cardiovascular disease (Foley et al 2012)

Methods

Results

Conclusion