Investigating the demographic history of Japan using ancient oral microbiota

Abstract

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’.

The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles

“…On the other hand, we did not identify significant differences between ancient samples that were grouped based on sex, age, and lifestyle. This result is consistent with previous studies [ 8 , 38 , 43 ] suggesting the relative stability in the composition of the oral microbiome at definite time points.…”

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

“…S9). The differential abundance of these AMR gene families was also observed in other prehistoric and historic samples from the literature (7,9,22,35), thus suggesting that methodological factors associated with laboratory procedures were most likely not responsible for the differences observed. The rpoC gene family was also discussed given its higher abundance in the ancient samples, except for those from Weyrich's study (9) (Datasets S12 and S13 and SI Appendix, Fig.…”

Insights into health and disease from ancient biomolecules

“…Tannerella forsythia may be a new example of an established outcome of colonialism, the fostering of a range expansion of more virulent pathogens. Eisenhofer et al [23] investigate human oral microbiomes of ancient Japan, specifically Jomon hunter-gatherers and Edo agriculturalists, who represent two time periods, each with distinct lifestyles. Despite the expectation that such a major lifestyle change should result in a microbiome shift as detected in prior gut microbiome studies [24], Eisenhofer et al [23] observed that the microbiome variation changed little between these periods, with a noteworthy exception of Edo-period differences between the sexes, which they propose reflects traditional cultural practices.…”

“…Eisenhofer et al [23] investigate human oral microbiomes of ancient Japan, specifically Jomon hunter-gatherers and Edo agriculturalists, who represent two time periods, each with distinct lifestyles. Despite the expectation that such a major lifestyle change should result in a microbiome shift as detected in prior gut microbiome studies [24], Eisenhofer et al [23] observed that the microbiome variation changed little between these periods, with a noteworthy exception of Edo-period differences between the sexes, which they propose reflects traditional cultural practices. In the third article, Achtman & Zhou [25] discuss recently developed bioinformatic tools for investigating microbial diversity in metagenomic datasets, and they use these to examine the oral microbiome from ancient dental calculus in addition to modern saliva and dental calculus samples across a broad geographical region.…”