Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan

Abstract

Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.

Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT

“…During the Edo era, brushing techniques and materials were not as advanced as the current ones. A report on DNA analysis of the food remains in human dental calculus from the Edo era in Japan using next-generation sequencing helped detect plant DNA of the genus Nicotiana ( Sawafuji et al, 2020 ). The use of tobacco has also been reported in the historical literatures in the Edo period ( Kitagawa, 1853 ; Miyazaki, 1967 ).…”

“…DNA extraction was performed in a dedicated ancient DNA laboratory at Tokyo University. To avoid contamination, DNA extraction was performed as described in a previous report ( Sawafuji et al, 2020 ).…”

“…However, the microbiome involved in the risk of disease development is regional ( Karlsson et al, 2013 ). There are a few reports regarding bacterial genomic analysis for the Japanese Edo era ( Eisenhofer et al, 2020 ; Sawafuji et al, 2020 ), and no studies discuss the oral microbiome related to periodontal disease using ancient calculus.…”

Shifting Baselines to Thresholds: Reframing Exploitation in the Marine Environment

“…For example, studies of dental calculus-calcified plaque on tooth remains-is a treasure trove of information on the ancient oral microbiome (Warinner et al, 2015). Analysis of dental calculus in human remains has revealed information on past diets, medicinal use, and ancient dental practices and associated cultural shifts (Blatt et al, 2011;Adler et al, 2013;Warinner et al, 2014;Sawafuji et al, 2020). As of yet no studies specifically link dental calculus to marine exploitation, but that does not preclude its potential applicability to understanding changing marine resources.…”

Helminth infection and human mobility in sambaquis: Paleoparasitological, paleogenetic, and microremains investigations in Jabuticabeira II, Brazil (2890 ± 55 to 1805 ± 65 BP)

“…Some techniques have been tested in an attempt to recover parasites and plants from archeological remains. The study of parasites and diet in archeological material has recently produced combined information about the health and survival conditions of the ancient populations (Moore et al, 2020; Sawafuji et al, 2020; Søe et al, 2018; Wiscovitch-Russo et al, 2020). The data achieved until now, however, could not provide direct information of helminth infection associated with burial in sambaquis archeological site.…”