Sample information.

Coprolites contain various kinds of ancient DNAs derived from gut micro-organisms, viruses, and foods, which can help to determine the gut environment of ancient peoples. Their genomic information should be helpful in elucidating the interaction between hosts and microbes for thousands of years, as well as characterizing the dietary behaviors of ancient people. We performed shotgun metagenomic sequencing on four coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. The coprolites were found in the layers of the Early Jomon period, corresponding stratigraphically to 7000 to 5500 years ago. After shotgun sequencing, we found that a significant number of reads showed homology with known gut microbe, viruses, and food genomes typically found in the feces of modern humans. We detected reads derived from several types of phages and their host bacteria simultaneously, suggesting the coexistence of viruses and their hosts. The food genomes provide biological evidence for the dietary behavior of the Jomon people, consistent with previous archaeological findings. These results indicate that ancient genomic analysis of coprolites is useful for understanding the gut environment and lifestyle of ancient peoples.

粪化石（Coprolites）蕴含源自肠道微生物、病毒及食物的各类古DNA，可用于解析古代人类的肠道环境。其基因组信息有助于阐明数千年来宿主与微生物间的互作关系，同时可刻画古代人类的饮食行为特征。本研究对从日本列岛鸟滨贝冢遗址（Torihama shell-mound site）出土的4件粪化石开展了霰弹宏基因组测序（shotgun metagenomic sequencing）。该批粪化石出土于绳文时代早期地层，地层学年代对应距今7000至5500年。经测序后，我们发现大量测序读段（reads）与现代人类粪便中常见的已知肠道微生物、病毒及食物基因组具有同源性。我们同时检测到多种噬菌体（phages）及其宿主细菌对应的读段，提示病毒与宿主曾共存。食物基因组为绳文人的饮食行为提供了生物学证据，与既往考古发现相符。上述结果表明，对粪化石开展古基因组分析，有助于理解古代人类的肠道环境与生活方式。