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Black Death plague pit produces first ancient bacterial genome

cemetary400.jpgBones uncovered in a medieval burial pit used to inter victims of the Black Death have yielded the first genome sequence of an ancient bacterial pathogen, the bubonic plague-causing bacterium Yersinia pestis.

The draft genome sequence, published online today in Nature, follows the publication of a short loop of Y. pestis DNA called the PCP1 plasmid from the same remains. That paper as well as a 2010 study that sequenced short stretches of Y. pestis DNA from different Black Death victims confirmed that bubonic plague was involved in one of history’s worst pandemics.

Yet neither sequence differs substantially from modern strains of Y. pestis, leaving open the question of why the Black Death was so severe, compared to more modern bubonic plague outbreaks. “We can’t find anything that makes the Black Death special,” says Johannes Krause, a paleo-geneticist at the University of Tübingen, Germany who led the study.


The Black Death emerged in Europe in 1347, probably from Asia, and quickly raced around the continent and to Britain, killing one-third to one-half of Europeans over the next five years. To cope with the thousands of bodies that would overwhelm existing cemeteries, London officials set aside two emergency burial pits on the outskirts of city. These cemeteries were used only during the Black Death.

A 1980s excavation of one plot, called East Smithfield, turned up one-quarter of the 2,400 bodies estimated to be buried there. Krause and his colleague Hendrik Poinar, of McMaster University in Hamilton, Ontario, and their team collected DNA from teeth and developed a way of fishing out the decayed and degraded plague sequences, leaving behind human and contaminating soil microbe DNA. A next-generation DNA sequencer decoded the plague fragments, producing most of the genome of the bacteria behind Black Death.

This sequence differs from the published genome reference strain of Y. pestis by about 100 DNA letters, however all of these changes are present in other plague strains circulating today, just not in the same combination. This would suggest that other epidemiological and environmental factors lay behind the ferocity of the Black Death, such as cold, wet weather and malnourishment, Poinar says.

By comparing the East Smithfield plague genome with those of 17 other plague strains circulating today, the researchers also conclude that the Black Death spawned other strains of Y. pestis that infect humans today. “What it means for us is that the human pathogenic plagues that we know today are all descendants of the medieval plague, of the Black Death,” Krause says.

This interpretation also raises questions as to what caused epidemics before the fourteenth century that are also termed plagues. The plague of Justinian, for instance, erupted in the sixth century Byzantine Empire and killed millions across Europe and western Asia. Krause and Poinar’s team suggest that these outbreaks were caused by now-extinct strains of Y. pestis or by entirely different pathogens.

Mark Achtman, a microbiologist at University College Cork in Ireland, questions this explanation. He says Krause and Poinar’s team did not analyze a whole family of Asian Y. pestis strains that infect humans and which may have origins more ancient than Black Death. Achtman speculates that one of these strains could be the descendant of the plague of Justinian.

Stay tuned to Nature’s news page next week for more on the Black Death.

Image of East Smithfield excavation copyright: Museum of London Archaeology

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