Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe—the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

考古牙结石或矿化斑块是追踪口腔微生物群随时间演变的关键工具，以响应影响我们文化和生物学的过程，例如新石器时代农业的兴起。然而，由于史前人类微生物组数据的缺乏，人类口腔菌群从史前到现在的变化程度仍然难以捉摸。在这里，我们展示了通过鸟枪法牙结石宏基因组学对来自两个地区的 44 名古代采集者和农民的口腔微生物组进行的重建，这两个地区在农业在整个欧洲的传播中发挥着关键作用——巴尔干半岛和意大利半岛。我们发现，南欧农业的引入并没有显着改变当地采集群体的口腔微生物组，尤其与奥尔森氏菌属物种的丰度增加有关。口腔分类群 807。史前人类口腔环境主要由微生物物种（Anaerolineaceae 细菌口腔分类群 439）主导，该微生物物种在地理上多样化。这种细菌共生体的近东谱系随新石器时代农民的传播而传播，并取代了当地采集者中存在的变种。我们的研究结果还表明，人类口腔微生物组组成的主要分类变化发生在新石器时代之后，并且现代人类的功能特征在近代不断进化，形成了以前不存在的特殊抗生素耐药机制。