Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.

中文翻译：

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青铜时代遗迹的古代基因组揭示了人类口腔病理生物的深层多样性和最近的适应性事件

古代微生物基因组可以阐明致病生物几千年来的进化，而牙齿提供了丰富的基质。然而，史前口腔致病生物多样性的表征是有限的。在欧洲，只有前农业时期的基因组经过了系统发育分析，没有与最近的考古时期相比。在这里，我们报告了爱尔兰石灰岩洞穴中两颗 4000 年前牙齿中保存完好的微生物组。其中含有与牙周炎有关的细菌，以及变形链球菌，这是龋齿的主要原因，在古代基因组记录中很少见。尽管源自同一个体，但这些牙齿产生了不同的连翘坦纳菌基因组，表明史前种群的菌株多样性水平较高。我们发现了微生物群失调的证据，与其他口腔链球菌相比，变形链球菌序列的数量不成比例。这种高丰度允许宏基因组组装，从而产生了第一个报道的古代基因组。系统发育分析表明，这两个物种在中世纪后都出现了人口大幅扩张，凸显了近期饮食变化的过度影响。在连翘中，这种扩张与较旧谱系的替换有关，可能反映了全基因组选择性扫描。因此，我们看到这一时期连翘的毒力库发生了巨大变化。变形链球菌表现出一种截然不同的模式，现代人群中仍然存在着截然不同的谱系。这可能是由于其高度重组的性质，允许通过选择性事件维持多样性。尽管如此，最近聚结的爆炸性增长和分离细菌素携带菌株的分支长度显着缩短表明变形链球菌种群和功能的重大变化与工业时期糖的普及相一致。