Ancient latrine sediments, which contain the concentrated collective biological waste of past whole human communities, have the potential to be excellent proxies for human gastrointestinal health on the population level. A rich body of literature explores their use to detect the presence of gut-associated eukaryotic parasites through microscopy, immunoassays and genetics. Despite this interest, a lack of studies have explored the whole genetic content of ancient latrine sediments through consideration not only of gut-associated parasites, but also of core community gut microbiome signals that remain from the group that used the latrine. Here, we present a metagenomic analysis of bulk sediment from medieval latrines in Riga (Latvia) and Jerusalem. Our analyses reveal survival of microbial DNA representative of intestinal flora as well as numerous parasites. These data are compared against parasite taxon identifications obtained via microscopy and ELISA techniques. Together, these findings provide a first glimpse into the rich prokaryotic and eukaryotic intestinal flora of pre-industrial agricultural populations, which may give a better context for interpreting the health of modern microbiomes.

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

古代厕所的沉积物含有过去整个人类社区集中的集体生物废物，因此有可能成为人口水平上人类胃肠道健康的良好代表。大量的文献探讨了它们如何通过显微镜，免疫测定和遗传学检测肠道相关的真核生物的存在。尽管有这种兴趣，但缺乏研究已经通过不仅考虑与肠道相关的寄生虫，而且还考虑了使用该厕所的人群留下的核心社区肠道微生物组信号，探索了古代厕所沉积物的全部遗传成分。在这里，我们对里加（拉脱维亚）和耶路撒冷的中世纪厕所中的大量沉积物进行宏基因组学分析。我们的分析揭示了代表肠道菌群以及许多寄生虫的微生物DNA的存活率。将这些数据与通过显微镜和ELISA技术获得的寄生虫分类单元进行比较。这些发现共同提供了对工业化前农业人口丰富的原核和真核肠道菌群的初步了解，这可能为解释现代微生物组的健康状况提供了更好的背景。

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。