BACKGROUND Dental 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. RESULTS Metagenomic 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. CONCLUSIONS Overall, 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.

中文翻译：

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牙菌斑和历史性牙结石之间的微生物差异与口腔生物膜的成熟阶段有关。

背景技术牙结石是钙化的口腔斑块生物膜，包含微生物和宿主生物分子，可用于研究历史性微生物组和宿主反应。如今，牙结石的积累通常不如历史上那么多，并且临床口腔微生物组研究主要集中在活体牙菌斑生物膜上。然而，牙菌斑和牙结石反映了口腔生物膜的不同状况，并且尚未系统地探索样品类型之间的微生物特性差异。在这里，我们比较了现代牙菌斑，现代牙结石和历史牙结石的微生物特征，以建立这些基质之间的预期差异。结果元基因组数据是根据现代和历史演算样本生成的，牙菌斑的宏基因组学数据可从“人类微生物组计划”中下载。评估了微生物组成和功能状况。元蛋白质组学数据是从历史演算样本的子集中获得的。微生物，蛋白质和代谢组学特征之间的比较显示，牙菌斑，现代牙结石和历史牙结石之间具有明显的分类学和代谢功能特征，但从健康牙齿和牙周病患牙齿收集的牙结石之间却没有。物种共排斥与生物膜环境有关。蛋白质组学分析显示，健康的牙齿样本中细菌毒力蛋白含量低，并且具有强大的先天免疫反应。蛋白质组学和代谢组学谱之间的相关性表明细菌脂质膜和膜相关蛋白的共同保存。