Ancient 5,500-Year-Old Treponema pallidum Genome Reconstructed in Colombia

Scientists have reconstructed the genome of Treponema pallidum – the bacterium responsible for syphilis and related illnesses – from approximately 5,500-year-old human remains found in Colombia.

The finding extends the pathogen’s confirmed genetic record by over 3,000 years. It also indicates that ancient treponemal bacteria in the Americas may have been more varied than those that circulate today.

The remains were recovered from a rock shelter in the Sabana de Bogotá area, close to present-day Bogotá. The research appeared in Science.

Put simply, these infections were not a recent arrival: they existed far earlier than genetic evidence had previously been able to establish.

“Our findings show the unique potential of paleogenomics to contribute to our understanding of the evolution of species, and potential health risks for past and present communities,” said geneticist Lars Fehren-Schmitz from the University of California, Santa Cruz (UCSC).

A cluster of almost-identical diseases

Today, T. pallidum is associated with three closely related forms of disease: syphilis, yaws and bejel, each caused by slightly different subspecies. Pinta, which predominantly affects the skin, is generally associated with Treponema carateum, although it is sometimes described as a relative of T. pallidum.

The difficulty is that these bacteria are genetically extremely alike. Their symptoms can differ greatly, while the differences in their DNA may be minimal.

Bones are not always decisive either. Treponemal diseases can produce skeletal changes, but these are neither consistent nor present in every case. Ancient DNA is therefore valuable because it can reveal relationships that skeletal evidence cannot.

The ancient form of a pathogen

In comparisons with contemporary T. pallidum strains, the ancient genome did not fit cleanly into any of the three established groups. It is unambiguously T. pallidum, yet appears to represent an early-diverging lineage: related to modern strains, but unlike those usually discussed.

This raises a compelling question: might it be linked to pinta, the poorly characterised member of the treponemal family?

Study co-author Anna-Sapfo Malaspinas leads a group at the SIB Swiss Institute of Bioinformatics.

“One possibility is that we uncovered an ancient form of the pathogen that causes pinta, which we know little about, but is known to be endemic in Central to South America and causes symptoms localized to the skin,” said Malaspinas.

“At this time, we cannot prove this is the case, but it is a lead worth investigating further.”

There is no conclusive classification so far. However, its failure to correspond with modern categories is precisely what makes the discovery notable.

A long evolutionary backstory

Genetic analysis suggests that this ancient lineage separated from other T. pallidum lineages roughly 13,700 years ago.

This does not mean the remains themselves are that old: the individual lived around 5,500 years ago. Rather, it indicates that the evolutionary branch represented by this strain is considerably older.

The researchers further estimate that the three modern subspecies separated at a later point, around 6,000 years ago. Taken together, these figures suggest that treponemal pathogens were evolving and branching across a lengthy period, with the Americas involved at an early stage.

Even so, the result does not settle the enduring debate over precisely where the disease syndromes originated.

Elizabeth Nelson, a molecular anthropologist and palaeopathologist at UCSC, pointed out that existing genomic evidence does not resolve the long-running question of where the disease syndromes themselves began.

“But it does show there’s this long evolutionary history of treponemal pathogens that was already diversifying in the Americas thousands of years earlier than previously known,” said Nelson.

“Our results push back the association of T. pallidum with humans by thousands of years, possibly more than 10,000 years ago in the Late Pleistocene,” said Davide Bozzi, a researcher at the University of Lausanne.

A surprise guest

The pathogen was detected almost unexpectedly. Initially, the researchers sequenced the individual’s DNA for a study of ancient human populations.

The work generated an exceptionally large dataset of about 1.5 billion DNA fragments, far more than is produced by most ancient-DNA projects.

In routine screening, two research teams – one at UC Santa Cruz and the other at the University of Lausanne – independently identified traces of T. pallidum.

The extensive depth of sequencing allowed them to reconstruct the pathogen genome without the dedicated enrichment procedures commonly required for ancient microbes.

More unexpectedly still, the skeleton had no apparent signs of treponemal disease. In addition, the sampled bone was a tibia, or shin bone, rather than a more usual choice such as teeth.

For future studies, this implies that visible lesions and ideal sample types may not be necessary to recover useful pathogen DNA when the quality of the data is sufficiently high.

Why this matters now

Reconstructing genomes from ancient pathogens is not merely an academic exercise. It enables scientists to examine how diseases evolve, how lineages diversify, and what forms of change could emerge again in the future.

A fuller understanding of a pathogen’s deep history also improves understanding of what it may be capable of.

Before publication, the team also sought to engage communities in Colombia, recognising that the material is not simply data but part of local human history.

“This process was essential because the findings are deeply connected to Colombia’s medical and cultural history,” Delgado explained.

“Engaging scholars, students, and Indigenous and non-Indigenous community members ensures the results are ethically communicated and interpreted in partnership with local communities.”

“This approach builds trust, supports responsible stewardship of sensitive discoveries, and reinforces local ownership of knowledge.”

Ultimately, the 5,500-year-old genome does more than extend a timeline: it suggests that the treponemal family tree may once have included branches that have not yet even been named.

The research is published in the journal Science.