Abstract:

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.

Key words: high-throughput sequencing, targeted enrichment technology, ancient pathogenic microorganisms, plague, genome