Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals

Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890–9,540 before present. The metagenomic profle exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identifed increased abundance of periodontitisassociated microbes. In addition, trained machine learning models predicted dysbiosis with 70–80% probability. Moreover, we identifed DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.

史前人类咀嚼过的松脂已被证实是获取古代人类及其微生物组（microbiome）古DNA的优质样本来源。本研究对瑞典赫瑟比克莱夫（Huseby Klev）出土的3件咀嚼松脂样本开展了宏基因组学（metagenomics）分析，这些样本的年代可追溯至距今9890至9540年前（before present，BP）。宏基因组特征揭示了中石器时代的口腔微生物组，其中包含机会致病性口腔病原菌。我们将该数据集与健康及生态失调（dysbiotic）的微生物组数据集进行比对，发现牙周炎（periodontitis）相关微生物的丰度显著升高。此外，经训练的机器学习模型以70%至80%的置信度预测了该口腔微生物组存在生态失调。不仅如此，我们还鉴定出赤狐、榛子、马鹿及苹果等真核生物的DNA序列。本研究结果表明，斯堪的纳维亚中石器时代存在口腔健康状况不佳的案例，同时证实咀嚼松脂样本可用于获取古代人类的材料使用情况、饮食结构及口腔健康相关信息。