Scientists have reconstructed a T. pallidum genome from a 5,500-year-old human burial in the Sabana de Bogotá region of Colombia, offering the earliest molecular evidence to date that this family of bacteria was present in the Americas thousands of years before European contact.
The discovery, reported in Science, comes from an adult male with an estimated age of 45 to 60+ years, who died around 5,500 years ago. The remains were excavated at Tequendama I, a Middle Holocene rock shelter with burials spanning roughly 10,000 to 2,300 years before present.
Treponemal infections include syphilis, yaws, and bejel – diseases that can leave characteristic skeletal damage in some cases. However, the Tequendama individual showed no visible bone changes consistent with treponematosis, underscoring one of the longstanding challenges of tracing these infections in the deep past: many cases may leave no clear skeletal evidence, and diagnostic bone lesions can overlap with other conditions.
Rather than targeting suspected infection, the researchers detected T. pallidum DNA during metagenomic screening of deep shotgun sequencing data originally generated for a human population genomics project. Although pathogen DNA represented only a tiny fraction of the dataset, the depth of sequencing allowed reconstruction of a draft bacterial genome (named TE1-3) at about 1.7× average coverage, spanning roughly 78 percent of the reference genome.
When the team compared TE1-3 to more than 100 modern and ancient treponemal genomes, phylogenetic analyses placed it as an early-diverging sister lineage to all known T. pallidum subspecies. This suggests the Colombian strain represents a previously unknown lineage, potentially a distinct subspecies, and indicates treponemal diversity in the Americas was broader than previously recognized.
Using molecular clock modeling, the researchers estimated that TE1-3 split from other T. pallidum lineages around 13,700 years ago, with diversification of the known subspecies occurring later within the Holocene.
Despite its age, TE1-3 appeared to contain virulence-associated genes seen in modern strains, suggesting it may have retained similar genetic capacity for infection.
Beyond its evolutionary implications, the finding highlights how metagenomic screening of ancient remains can reveal infections that would otherwise go undetected – helping close the gap between skeletal evidence of disease and the molecular history preserved in ancient DNA.
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