The study uses genetic data from 1,313 ancient human remains, spanning a period of 37,000 years, to construct a comprehensive spatiotemporal map of ancient human infections across Eurasia. Human populations have suffered a lot from infectious diseases throughout history, but major issues about their origins and historical dynamics remain unanswered. By applying shotgun-sequencing data to ancient human DNA and using a high-throughput computational approach, researchers discovered 5,486 validated microbial deoxyribonucleic acid (DNA) sequences from 492microbial species, including 3,384 associated with known human diseases.
To represent diverse archaeological backgrounds, the samples primarily originated from western Eurasia (77%), central/north Asia (20%), and southeast Asia (3%). Recent advances in ancient pathogen genomes offer direct genetic evidence of past microbial infection. These approaches have led to unexpected results for some of the most significant infectious diseases in human history.
Within and between genera, researchers found major variations in the distributions of the ancient microbial sequences’ genetic closeness to modern reference genomes. Between species, the rate of read mapping varied by orders of magnitude, ranging from lower limits of detection to species with high read recruitment. Pathogens with a high average nucleotide identity (ANI) and a low multi-allele rate were frequently observed in species, suggesting that infections were dominated by a single, prevalent strain. Â
The prevalence of plague in Europe during this time was shown by the identification of 11 out of 42 cases from two Denmark cemeteries who lived in the late medieval and early modern periods. The bacterium Mycobacterium leprae, which causes leprosy, was discovered in 7 Scandinavian people. It is difficult to identify eukaryotic infections due to their huge and fragmented reference genomes, which were often contaminated with sequences from other organisms. Hepatitis B virus (HBV) was detected in 28 individuals from Siberia, along with Torque teno virus, which was found in one Neolithic individual. Regarding malaria, nine infections were documented, including one case of Plasmodium falciparum in Armenia.
During ancient human populations, coinfections were common and may have contributed to increased morbidity and mortality. Researchers applied time series decomposition and Bayesian change-point detection to assess temporal shifts in the incidence of two highly detectable pathogens. This shift suggests a high risk of zoonotic disease transmission that will promote the spread of both novel and established infections.
A higher genetic vulnerability to disease or frequent illness was linked to the pastoralist lifestyle, considered a primary cause of the high infection rate in Steppe populations. As human teeth are exposed to the oral cavity, they show better access to microbial DNA in the bloodstream. Thus, they were able to maintain pathogen DNA and the ancient oral microbiome better than petrous bones. This study explains how cultural shifts, such as farming and migration, reshaped the ancient infectious disease landscape, providing genomic evidence for the co-evolution of humans and diseases.
Reference: Sikora M, Canteri E, Fernandez-Guerra A, et al. The spatiotemporal distribution of human pathogens in ancient Eurasia. Nature. 2025. doi:10.1038/s41586-025-09192-8
