Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan
Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan
复制标题
DOI：
10.1371/journal.pone.0226654
复制
发表时间：
2018-03
期刊：
影响因子：
3.7
通讯作者：
Rikai Sawafuji;Aiko Saso;W. Suda;M. Hattori;S. Ueda
中科院分区：
文献类型：
--
作者：
Rikai Sawafuji;Aiko Saso;W. Suda;M. Hattori;S. Ueda
目的：虽然有许多方法可以重建过去的饮食，但详细的分类鉴定仍然具有挑战性，大多数植物几乎不会留在一个地点。在这项研究中，我们应用DNA元条形码的牙结石江户人的食物种类的分类鉴定。材料与方法：从日本江户时代云古院遗址（18 - 19世纪世纪）的13个人牙结石中提取DNA。聚合酶链反应（PCR）和测序使用稻属特异性引物组进行，因为水稻（Oryza sativa）是主食，并且这是当时日本唯一存在的该属的成员。针对植物、动物（肉和鱼）和真菌的DNA元条形码也被用于调查膳食多样性。结果：PCR和桑格测序结果表明，超过一半的样品中检测到稻属的扩增产物。DNA元条形码使我们能够识别植物和真菌的分类群，虽然动物的分类群没有检测到，除了人类。讨论内容：大多数植物分类群都存在于日本，包括当时作为食物食用的物种，如历史文献所证实的。其他群体在江户人的生活方式中占有重要地位，例如用于医疗目的和烟草。结果表明，植物DNA分析从结石提供了有关食物多样性和生活习惯的信息，从过去，可以补充其他分析方法，如淀粉分析和稳定同位素分析。
Objectives: 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 Edo people for the taxonomic identification of food species. Materials and Methods: 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 was also carried out to investigate dietary diversity. Results: 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. Discussion: Most of the plant taxonomic groups are present in Japan and include 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 starch analysis and stable isotope analysis.