Ancient Treponema pallidum Genome Recovered From 5,500-Year-Old Skeleton

Researchers have extended the known genetic history of Treponema pallidum, the bacterium responsible for several treponemal diseases, by analyzing ancient DNA from a prehistoric human skeleton in South America.

The study focused on a 5,500-year-old individual from Sabana de Bogotá, Colombia, whose remains provided the oldest known T. pallidum genome to date. This discovery adds approximately 3,000 years to the previous genetic record for the bacterium.

Through phylogenetic analysis, the research team determined that the ancient genome belongs to a previously unidentified branch of T. pallidum, which diverged before the emergence of modern subspecies. The genome includes all virulence-associated genes found in current strains, indicating the presence of similar pathogenic features thousands of years ago.

The ancient DNA was extracted from a tibia fragment using deep shotgun sequencing techniques. Despite the pathogen DNA making up less than 0.002% of the total genetic material, researchers were able to recover a complete genome for further study.

What the numbers show

• The ancient genome is about 5,500 years old
• The genetic record of T. pallidum has been extended by roughly 3,000 years
• Researchers estimate the lineage diverged around 13,700 years ago

According to the study, the individual’s skeleton did not display the bone lesions commonly linked to treponemal disease, yet the presence of T. pallidum DNA was confirmed. This suggests that infection can be detected even when skeletal evidence is absent.

The findings indicate that treponemal diseases circulated in the Americas long before European contact and prior to the development of agriculture in the region. The research provides new insight into the early evolution and spread of these pathogens.

The results were published in the journal Science on 22 January 2026, offering a new perspective on the history of infectious diseases in ancient human populations. The study demonstrates the value of ancient DNA analysis for understanding the origins and diversity of disease-causing organisms.

* This article is based on publicly available information at the time of writing.