Scientists from the University of Lausanne have reconstructed the genome of Treponema pallidum, the bacterium responsible for syphilis and other treponemal infections, from 5,500-year-old human remains found in Sabana de Bogotá, Colombia. Reported in Science, the finding extends the known genetic timeline of this pathogen by over 3,000 years and provides new insight into its long evolutionary relationship with humans.
The individual’s skeleton, recovered from a rock shelter near Bogotá, offered remarkably well-preserved genetic material. Researchers initially sequenced the person’s DNA to study human population history, producing about 1.5 billion genetic fragments—an unusually deep dataset compared to most ancient DNA projects. During screening, teams at the University of California, Santa Cruz, and the University of Lausanne independently identified traces of T. pallidum DNA. The pathogen accounted for only a tiny fraction of the genetic data, yet the extensive sequencing coverage enabled scientists to reconstruct its full genome without relying on enrichment techniques typically required for ancient bacterial DNA.
The bacterial DNA was recovered from a tibia, a bone type not commonly used for pathogen sequencing. The skeleton showed no visible signs of treponemal infection—an important indication that ancient microbial DNA can be found even in individuals without skeletal evidence of disease. This approach suggests future sampling strategies could expand beyond bones showing visible signs of disease.
Comparative genomic analyses confirmed that the recovered strain belongs to T. pallidum but does not match any of the modern subspecies that cause syphilis, yaws, or bejel. Genetic modeling indicates that this ancient lineage diverged from other T. pallidum forms roughly 13,700 years ago, while the three modern lineages split only about 6,000 years ago. This early branching pattern implies that treponemal pathogens were already genetically diversifying in the Americas thousands of years before previously recognized.
The work reflects the combined expertise of archaeologists and geneticists analyzing remains from the Tequendama 1 site. The unexpected presence of T. pallidum in this individual underscores how high-throughput sequencing and deep genomic sampling can reveal hidden pathogen histories, offering critical reference points for understanding how infectious organisms evolved alongside humans.
Publication details: Davide Bozzi et al., A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia.Science391,eadw3020(2026).DOI:10.1126/science.adw3020
https://www.science.org/doi/10.1126/science.adw3020
The individual’s skeleton, recovered from a rock shelter near Bogotá, offered remarkably well-preserved genetic material. Researchers initially sequenced the person’s DNA to study human population history, producing about 1.5 billion genetic fragments—an unusually deep dataset compared to most ancient DNA projects. During screening, teams at the University of California, Santa Cruz, and the University of Lausanne independently identified traces of T. pallidum DNA. The pathogen accounted for only a tiny fraction of the genetic data, yet the extensive sequencing coverage enabled scientists to reconstruct its full genome without relying on enrichment techniques typically required for ancient bacterial DNA.
The bacterial DNA was recovered from a tibia, a bone type not commonly used for pathogen sequencing. The skeleton showed no visible signs of treponemal infection—an important indication that ancient microbial DNA can be found even in individuals without skeletal evidence of disease. This approach suggests future sampling strategies could expand beyond bones showing visible signs of disease.
Comparative genomic analyses confirmed that the recovered strain belongs to T. pallidum but does not match any of the modern subspecies that cause syphilis, yaws, or bejel. Genetic modeling indicates that this ancient lineage diverged from other T. pallidum forms roughly 13,700 years ago, while the three modern lineages split only about 6,000 years ago. This early branching pattern implies that treponemal pathogens were already genetically diversifying in the Americas thousands of years before previously recognized.
The work reflects the combined expertise of archaeologists and geneticists analyzing remains from the Tequendama 1 site. The unexpected presence of T. pallidum in this individual underscores how high-throughput sequencing and deep genomic sampling can reveal hidden pathogen histories, offering critical reference points for understanding how infectious organisms evolved alongside humans.
Publication details: Davide Bozzi et al., A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia.Science391,eadw3020(2026).DOI:10.1126/science.adw3020
https://www.science.org/doi/10.1126/science.adw3020