Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution.

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

人类微生物组研究越来越多地结合宏观生态学方法，例如群落组装、网络分析和功能冗余，以更全面地表征微生物组。此类分析尚未应用于古代人类微生物组，阻碍了对人类微生物组进化的深入了解。我们通过分析已发表的古代微生物组数据集来解决这个问题：来自 Rio Zape（n = 7；700 CE 墨西哥）和历史牙结石（n = 44；1770-1855 CE，英国）的粪化石，以及两个新的牙结石数据集：玛雅人（n = 7；公元前170-885 年，伯利兹）和努拉吉撒丁人（n = 11；公元前 1400-850 年，意大利）。牙周炎相关细菌（Treponema denticola，Fusobacterium nucleatum和Eubacterium saphenum ) 被确定为牙结石数据集中的关键分类群。粪化石基石分类群包括已知的短链脂肪酸生产者（双形真杆菌、琥珀酸杆菌）和潜在的疾病相关细菌（埃希氏菌、短螺旋体）. 古代和现代微生物组之间生态特征的重叠通过当代狩猎采集者和古代粪化石之间功能反应多样性特征的相似性以及古代玛雅人、历史悠久的英国和现代西班牙牙结石之间的相似性来表明；然而，古老的 Nuragic 牙结石显示出独特的生态结构。我们从古代微生物组数据中检测到关键的生态特征，为扩大对人类微生物组进化的理解铺平了道路。

这篇文章是主题问题“从古代生物分子洞察健康和疾病”的一部分。