While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species—Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

虽然人体微生物群落（微生物群）现在通常与工业化人口中的健康和疾病相关，但我们对这些微生物群落在整个历史和深厚的史前时期如何与人类共同进化和变化的了解甚少。现在，我们可以通过对钙化牙菌斑（牙结石）中保存的古代DNA进行测序来检查这些群落，从而深入了解疾病的起源及其与人类历史的联系。在这里，我们研究了保存在牙结石样本中的远古DNA及其与日本的两个主要文化时期的联系：绳纹时期的狩猎者-采集者目前约有3000年（BP）和江户时代的农学家400-150 BP。我们调查了日本的人类口腔微生物群随时间变化的情况，并探讨了日本古代人口中与口腔疾病（例如牙周病，龋齿）相关的微生物的存在。最后，我们通过对广泛保存的口腔物种进行系统生物学分析，探讨了口腔微生物菌株的多样性及其与古代日本古代人口学的潜在联系，Anaerolineaceae口腔类群439.据我们所知，该研究代表了对日本古代口腔微生物组的首次研究，并表明对古代牙结石的分析可提供有关非传染性疾病起源及其与人类人口统计学渊源的重要信息。 。

本文是“从古代生物分子对健康和疾病的洞察”这一主题问题的一部分。