Scientists have recovered a genome of Treponema pallidum – the bacterium whose subspecies today are responsible for four treponemal diseases, including syphilis – from 5,500-year-old human remains in Sabana de Bogotá, Colombia. The research expands knowledge about the history of this infectious disease and its occurrence in human populations, with findings now published in the journal Science.
The individual was archaeologically recovered from a rock shelter near Bogotá, Colombia, dating back roughly 5,500 years. The discovery pushes the genetic record of this pathogenic species back by more than 3,000 years, strengthening evidence that these infections have circulated in the Americas far longer than previously known.
"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 at the University of California, Santa Cruz.
What are treponemal diseases?
Treponema pallidum is a spiral-shaped bacterium that exists in three closely related forms today, each responsible for a different disease: syphilis, yaws and bejel. A fourth treponemal disease, pinta, is caused by Treponema carateum or Treponema pallidum subsp. carateum, but no genome for this pathogen has yet been recovered, casting doubts about its phylogenetic relationships and taxonomic classification.
Although the three T. pallidum subspecies are nearly identical genetically, scientists do not know when or how the different disease forms emerged. Some data exists about the evolutionary history of pathogens, but there remain significant gaps between what skeletal remains reveal and what genetics can confirm.
For the study, the research team demonstrated that the ancient DNA recovered belongs to the Treponema pallidum species, but it does not match any of the genetically known forms that cause disease today. The scientists showed that while it is closely related, it diverged early in the evolutionary tree.
"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 Anna-Sapfo Malaspinas at the University of Lausanne and group leader at the SIB Swiss Institute of Bioinformatics. "At this time, we cannot prove this is the case, but it is a lead worth investigating further."
Scientists estimate this ancient strain split from other T. pallidum lineages about 13,700 years ago. The three modern subspecies, by comparison, diverged much more recently, about 6,000 years ago, which aligns with previous research. These findings shed new light on how diverse these pathogens were in the past and serve as a reference point for understanding when they began branching into different forms.
"Current genomic evidence, along with our genome presented here, does not resolve the long-standing debate about where the disease syndromes themselves originated, 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 Elizabeth Nelson, a molecular anthropologist and paleopathologist at SMU.
A genetic puzzle
Understanding how treponemal diseases emerged and how treponemal pathogens evolved is surprisingly complicated because the bacteria are almost identical genetically, yet they get transmitted differently and can vary in clinical presentation.
"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 researcher Davide Bozzi at the University of Lausanne and SIB Swiss Institute of Bioinformatics.
This discovery builds on years of collaborative archaeological and genomic research at the Tequendama 1 site. Archaeologist Miguel Delgado at the Universidad Nacional de La Plata in Argentina and Fehren-Schmitz had previously published work offering detailed context about the skeleton.
The finding emerged unexpectedly. Researchers originally sequenced the individual's DNA to study human population history, generating 1.5 billion fragments of genetic data—far more than typical studies. While screening the data, teams at the University of California, Santa Cruz and the University of Lausanne independently detected T. pallidum and joined forces to investigate. The bacterial DNA made up only a tiny fraction of the genetic material, but the unusually deep sequencing allowed researchers to reconstruct the genome without the specialized techniques normally required.
The three diseases caused by T. pallidum (bejel, yaws, and syphilis) can leave marks on bones, but only at certain stages and not in every infected person. Most ancient T. pallidum genomes have been recovered from teeth or bones of people with clear signs of infection, but this skeleton showed none. Researchers sampled a tibia, or shin bone, a skeletal element not typically used for ancient DNA extraction. The approach paid off, suggesting that even bones without visible signs of disease could be valuable sources of pathogen DNA.
Researchers believe understanding how infectious diseases emerged and evolved in the past could help scientists predict how they may change in the future and help societies prepare for what lies ahead.
Before publishing, the researchers shared their findings with communities in Colombia, recognizing the discovery's significance to the country's medical history. They consulted with local scholars, students and community members, and connected with stakeholders through presentations and interviews. The team also obtained all necessary permits for exportation and study.
"This process was essential because the findings are deeply connected to Colombia's medical and cultural history," said Delgado. "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."
In addition to Nelson, Bozzi, Malaspinas, Delgado and Fehren-Schmitz, Nasreen Broomandkhoshbacht, now at the University of Vermont, also co-led the research, working with Kalina Kassadjikova of the University of California, Santa Cruz; Jane Buikstra of Arizona State University; Carlos Eduardo G. Amorim of California State University, Northridge; Melissa Estrada Pratt of the Instituto Colombiano de Antropología e Historia in Bogotá, Colombia; Gilbert Greub of the University of Lausanne and Lausanne University Hospital in Switzerland; Nicolas Rascovan of the Institut Pasteur in Paris; and David Šmajs of Masaryk University in the Czech Republic.
