Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

中文翻译：

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古代细菌 DNA 的过去、现在和未来。

20 世纪 80 年代中期进行的开创性研究证明了对古代 DNA (aDNA) 进行测序的可能性，这使我们能够回答有关人类过去的基本问题。因此，微生物学家获得了一个强大的工具，可以直接了解难以理解的细菌历史，而迄今为止，由于化石记录匮乏，这些历史还无法实现。最初受到污染问题的困扰，该领域随着技术进步而发展，高通量测序的出现成为序列输出和验证方面的突破。尽管面临着细菌分析特有的挑战，但越来越多的可行 aDNA 来源为微生物研究开辟了多种途径。人们从骨头、牙髓、木乃伊和历史医学标本中提取了古代病原体，并回答了一些焦点历史问题，例如将黑死病的病原体确定为鼠疫耶尔森氏菌。此外，来自化石粪便、木乃伊和牙菌斑的古代人类微生物组显示出，随着新石器时代的人口转型和工业革命，人类共生体发生了变化，而来自永久冻土样本的环境分离物则显示出古代抗菌素耐药性的迹象。细菌aDNA研究的迅速扩大，最终导致古代基因组库不断增长，也使得古代基因组与现存基因组的比较成为可能，阐明了细菌的进化史。在这篇综述中，我们总结了当前的研究途径，并将它们与该领域过去的背景联系起来，同时也指出了仍有待回答的问题。