Geneticists from KU Leuven and international colleagues have conducted the largest ancient DNA study ever performed on human remains from a single medieval burial site. In total, they analysed the remains of 400 individuals buried between the 8th and 18th centuries beneath what is now the main square (Groenmarkt) of Sint-Truiden, a historic town in present-day Belgium. The study offers unprecedented insights into how migration, urban development, family structures, and epidemics shaped the genetic landscape of this medieval city and of the broader Low Countries. Remarkably, it also uncovered the first direct evidence of the plague in medieval Flanders, at a time when no written sources from the town make mention of the disease.

Sint-Truiden originated in the 7th century around an abbey founded by Saint Trudo. After his death in 693, the abbey developed into an influential pilgrimage site, attracting visitors from afar and giving rise to a prosperous trading town with international ties. Thanks to a well-preserved monastic chronicle, the historical outline of Sint-Truiden is fairly well known. Now, the DNA of its former inhabitants provides a new chapter to that story. During archaeological excavations in 2019, more than 3,000 skeletons were uncovered beneath the town square, once the parish cemetery of the Church of Our Lady, located in the shadow of the abbey.

A team led by Professor Toomas Kivisild and Professor Maarten Larmuseau (KU Leuven), together with Professor Christiana Scheib (Cambridge University), selected 400 skeletons for DNA analysis. Never before has such a large number of ancient DNA samples been studied from a single site anywhere in the world.

One medieval town, one thousand years of genetic memory

The results reveal a unique genetic timeline spanning a thousand years. In the early Middle Ages (8th to 10th centuries), the population of Sint-Truiden was markedly more genetically diverse than in later periods.

‘At that time, the genetic differences between regions within present-day Flanders were almost as large as those between present-day Belgians and Spaniards,’ says Owyn Beneker, PhD student at KU Leuven and first author of the study.

Particularly striking is the presence of five individuals with genetic profiles closely resembling those of historical populations from Ireland or Scotland, which were found in the oldest layers of the cemetery. From the 11th century onward, genetic diversity gradually decreased and the population became more homogeneous. The DNA of Sint-Truiden’s later inhabitants strongly resembles that of modern-day residents of the Limburg province.

According to Professor Toomas Kivisild, the findings show how the genetic structure of the Low Countries resulted from centuries-long mixing between two major ancestral groups: one of ‘Gaulish’ origin and one of ‘Germanic’ origin. ‘This admixture underlies the north–south genetic gradient we still observe today in both Belgium and the Netherlands,’ Kivisild explains.

The team also found correlations between ancestry and specific genetic traits. Individuals with more Germanic ancestry were more likely to carry variants associated with red hair, while those with more Gaulish ancestry were more likely to carry a gene variant linked to higher vitamin D levels in the blood.

First direct traces of the plague in medieval Flanders

The study also yielded the first direct evidence of the plague (Yersinia pestis) in medieval Flanders. In five individuals dated to the 14th century, DNA of the plague bacterium was detected. These individuals were buried in scattered, individual graves, not in mass graves as often associated with plague victims.

‘There is no written record of the plague affecting Sint-Truiden in the 14th century, but we find it in the DNA,’ says Professor Maarten Larmuseau. ‘It shows how genetic research can uncover hidden chapters of history.’

Interestingly, the plague seems to have had little long-term genetic impact. The researchers found no signs of lasting shifts in the population’s immune gene diversity following the epidemic.

The study also brought surprising results regarding biological kinship. Out of 400 individuals, only a small number were found to be closely related—remarkably fewer than in other studied medieval cities, such as Cambridge (UK). Only in the oldest part of the cemetery, especially near the abbey, relatives were more frequently buried together. This suggests that grave allocation was not random in medieval times, but likely reflected social status or ties to the abbey community.

‘For the first time, we have been able to reconstruct patterns of migration, kinship and disease in such depth and scale within a single medieval city,’ Larmuseau concludes. ‘This cemetery in Sint-Truiden offers a unique genetic window into a thousand years of history in the Low Countries.’