Scientists have successfully reconstructed the genome Treponema pallidum from human remains that are about 5,500 years old discovered in the Sabana de Bogotá region of Colombia. This bacterium is responsible for several serious infectious diseases today, including syphilis. Findings published in journal Sciencethey significantly expand what scientists know about how long these infections have affected the human population.
The remains were excavated from a rock shelter near present-day Bogotá and date back to around 5,500 years ago. By identifying this ancient genome, scientists expanded the known genetic history Treponema pallidum more than 3000 years. The evidence adds weight to the idea that treponemal disease circulated in the Americas much earlier than previously documented.
“Our findings demonstrate the unique potential of paleogenomics to contribute to our understanding of species evolution and potential health risks to past and present communities,” said geneticist Lars Fehren-Schmitz of the University of California, Santa Cruz.
What are treponemal diseases?
Treponema pallidum is a spiral-shaped bacterium that exists today in three closely related subspecies. Each causes a different disease: syphilis, yaws and bejel. A fourth treponemal disease, pinta, is caused Treponema carateum or Treponema pallidum subsp. karate. No complete genome of the pathogen responsible for pint has yet been obtained, leaving questions about its evolutionary relationships and classification.
Despite their nearly identical genetic make-up, scientists still don’t know when or how these different forms of the disease arose. While skeletal remains can sometimes show signs of infection, genetics often tell a more complex story. Large gaps remain between what the bones can reveal and what ancient DNA can confirm about the development of the disease.
A lost lineage of a known pathogen
In this study, scientists confirmed that the ancient DNA belonged to this species Treponema pallidumbut it did not correspond to any of the known forms that cause disease today. Although the ancient genome is closely related to modern strains, it split off early in the bacterium’s evolutionary history.
“One possibility is that we have uncovered an ancient form of the pathogen that causes pinto, about which we know little, but is known to be endemic in Central to South America and to cause symptoms localized to the skin,” said Anna-Sapfo Malaspinas from the University of Lausanne and group leader at the SIB Swiss Institute of Bioinformatics. “We can’t prove that’s the case at this point, but it’s a clue worth investigating further.”
Based on genetic analysis, scientists estimate that this ancient strain split from the others T. pallidum lines about 13,700 years ago. In contrast, the three modern subspecies appear to have diverged much later, around 6,000 years ago. These timelines support earlier research and highlight how different treponemal pathogens were in the distant past.
“The 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 that there is a long evolutionary history of treponemal pathogens that diversified in the Americas thousands of years earlier than previously known,” said Elizabeth Nelson, a molecular anthropologist and paleopathologist at SMU.
A genetic puzzle with modern implications
Tracing the origins of treponemal diseases is particularly challenging because the bacteria are extremely similar at the genetic level. At the same time, they spread in different ways and can cause very different symptoms, making it difficult to untangle their evolutionary paths.
“Our results refute the association T. pallidum with humans by thousands of years, perhaps more than 10,000 years ago in the late Pleistocene,” said researcher Davide Bozzi of the University of Lausanne and the SIB Swiss Institute of Bioinformatics.
The discovery builds on long-term archaeological and genetic work at the Tequendama 1 site. Earlier studies by archaeologist Miguel Delgado of the Universidad Nacional de La Plata in Argentina and Fehren-Schmitz provided detailed background on the skeleton itself.
An unexpected finding in large-scale DNA data
The pathogen was not initially discovered on purpose. Researchers originally sequenced an individual’s DNA to study the ancient history of human populations, creating about 1.5 billion fragments of genetic data, far more than usual. During a routine screening, teams from the University of California, Santa Cruz and the University of Lausanne independently detected the tracks T. pallidum and decided to explore it together.
Although the bacterial DNA made up only a small part of the total genetic material, the depth of the sequencing allowed the team to reconstruct the pathogen’s genome without using specialized enrichment techniques.
Diseases caused T. pallidum (bejel, yaws, and syphilis) can leave marks on bones, but only under certain conditions and not in all infected individuals. Most of the ancient genomes of this bacterium were obtained from teeth or bones that clearly showed signs of disease. In this case, the skeleton showed no visible signs of infection. The researchers took a sample of a tibia, or tibia, which is not normally used for ancient DNA studies. The success of this approach suggests that even bones without obvious disease markers can retain valuable genetic information.
Why the history of ancient diseases is important today
Scientists hope that by learning how infectious diseases have emerged and changed in the past, they can better predict how they might evolve in the future. This knowledge could help modern society prepare for potential health threats.
Before publishing the results, the research team shared their findings with communities in Colombia, acknowledging the importance of the discovery to the country’s medical history. They consulted local scientists, students and community members and engaged with stakeholders through presentations and interviews. All necessary permits for export and study have been obtained.
“This process was crucial because the findings are deeply connected to Colombia’s medical and cultural history,” Delgado said. “Involving scientists, students and Indigenous and non-Indigenous community members ensures that results are ethically communicated and interpreted in partnership with local communities. This approach builds trust, promotes responsible management of sensitive discoveries and strengthens local ownership of knowledge.”
International cooperation
In addition to Nelson, Bozzi, Malaspinas, Delgado and Fehren-Schmitz, the research was led by Nasreen Broomandkhoshbacht, now at the University of Vermont. The broader team included Kalina Kassadjik from 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 from Masaryk University in the Czech Republic.
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