古代病原微生物基因组研究对病理学、微生物学、考古学等领域均具有重要的价值。在过去的十年里,高通量测序和靶向富集技术的发展和应用使古代微生物基因组的获取成为可能,通过对古代人群样本中获取的宏基因组进行筛查,使得引发古代疫情的相关病原体的基因组得以重建,为研究人类传染病的起源、传播和演化提供了一个独特的窗口。在当今全球化的背景下,新发及再发传染性疾病的出现频率促使我们回顾过去,以便更好地了解现代病原菌出现和古代病原菌重新出现的过程和生态环境。在这篇文章中,我们总结了近十年古代病原微生物基因组水平的研究进展,并提出了这项研究所面临的挑战以及未来的研究前景和方向。

Terrible epidemic disasters, such as the Black Death and smallpox, have run through the history of human society and have had a major impact on the development of human civilization and even the rise and fall of dynasties. Obtaining and analyzing the genomes of pathogens from major ancient outbreaks can not only reveal the causes of formation behind the devastating historical catastrophes of the era, but also be traced to the geographic spread and evolutionary patterns of pathogens, with important implications for the fields of pathology, microbiology, and archaeology.

In this review, we first briefly introduce the plague disasters that occurred in history and their impact on human history, and then introduce traditional research methods on ancient plagues, including philology and paleopathology. We also point out the limitations of these traditional studies, such as differences in ancient and modern medical knowledge systems that make it difficult to draw firm conclusions from historical records, and morphological studies that are difficult to detect for those that do not cause overt skeletal damage.

In the past decade, the development and application of high-throughput sequencing have made it possible to recover ancient DNA, although we still need pay a lot attention to exogenous contamination, the ancient pathogen genome characterized by high degradation and low abundance can be retrieved by targeted enrichment technologies and powerful computational approach. Reconstructed pathogen genomes provide a unique window into the origin, spread, and evolution of human infectious diseases. In today’s globalized context, the frequency of emerging and re-emerging infectious diseases prompts us to look back at past epidemics, which can help us better understand the processes and ecology of the emergence of modern pathogens and the re-emergence of ancient pathogens. we briefly describe the wet-lab procedures and analytical approaches used to study the microbial composition of ancient samples, and summarize studies Progress of ancient pathogen genomes using the study of ancient Yersinia pestis and Salmonella enterica genomes as examples, and exibit these studies have provide us the new insights to pathogen evolution, antibiotic resistance, and ancient health, cultural practices, and historical epidemics. Finally, we also propose the challenges facing this research and future research prospects and directions.