Abstract
BackgroundDental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.ResultsMetagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.ConclusionsOverall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.
Highlights
Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses
In order to advance the studies of oral microbiome evolution, it is necessary to understand the basis of observed differences between the microbial profiles of ancient dental calculus and modern dental plaque
MapDamage plots of reads that mapped to the genome of the oral bacterium Tannerella forsythia, a species both prevalent and abundant in historic dental calculus, and to the human genome display elevated C to T transitions at molecule ends (Additional file 1: Figure S2), indicative of deamination, a pattern typical of authentic ancient DNA
Summary
Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. During the course of biofilm growth and maturation, oxygen is progressively depleted and proteolytic obligate anaerobes, including methanogens and sulfate-reducers, rise in abundance [16], resulting in the formation of a fully mature oral biofilm profile. This mature community is likely the biofilm stage historically preserved in dental calculus. The microbial profiles of ancient dental calculus often contain high proportions of proteolytic obligate anaerobes, including Tannerella, Porphyromonas, Methanobrevibacter, and Desulfobulbus [1, 2], and resemble a fully mature oral biofilm. This potentially makes a direct comparison with contemporary dental plaque, especially plaque regularly disrupted by oral hygiene regimens, more complicated
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