Unlocking the Secrets of the Black Death: Mysteries of Yersinia Pestis

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The Plague is caused by the bacterium Yersinia pestis. There are three extremely well-known pandemics; the first well-documented crisis was the Plague of Justinian. The most infamous, with the highest estimated death toll, was the Black Death. Then came the Great Outbreak of London as a result of the migration of the bacteria. Yersinia pestis is the lethal bacterium known for killing an estimated 70-200 million people in Europe, Asia, and Africa during the Black Death. Scientists concluded that even though the Plague originated in Asia, it was likely that the fleas that lived on rats, called Xenopsylla cheopis, transported this disease to the other two continents. The two different types include primary bubonic Plague and septicemic Plague. Plague bacteria are most often transmitted by the bite of an infected flea.

Tracing the Footprints of Death: Historical Pandemics

During plague epizootics, many rodents died, causing hungry fleas to seek other sources of blood. The enzootic cycle was when the Y. pestis was able to circulate at low rates within populations of rodents, mostly undetected because it didn’t produce an outbreak. When the bacteria pass to other species during an epizootic cycle, humans face a greater risk of becoming infected with plague bacteria. People and animals that were near areas where dead infected animals were were at risk of being infected from flea bites. Dogs and cats also plague-infected fleas into homes.

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From the teeth of plague victims, scientists have pieced together a family tree of Y. pestis, discovering that the strain from the Justinian Plague was related to, but distinct from, other strains of the Plague. Scientists discovered last year, during the construction of the new cross-rail underground rail link beneath London, recovered DNA of Yersinia pestis from skeletons from the Great Outbreak of London. The DNA was identified by teams of scientists from the Museum of London Archeology (MOLA) and the Max Plank Institute in Germany.

Tooth enamel preserved the genetic information of any bacteria that was circulating in the individual’s bloodstream at the time of death. The bacteria perished shortly after its host did, so the remains posed no risk. Stable isotope analysis of strontium (a highly chemically reactive element) and oxygen in the individuals’ teeth enabled scientists to learn if they were native Londoners or if they moved to the city from elsewhere. Carbon and nitrogen isotopes revealed how much meat, vegetables, and seafood they ate. Microbiome DNA from their teeth helped to further determine which airborne particles and pollutants they ingested in life.

Unlocking the Genetic Secrets: From Ancient Victims to Modern Revelations

Many scientists believed that the Y. pestis could not have been the cause of the Plague because of how mild other Bubonic plagues were in comparison to ancient outbreaks like the Black Death. A team led by Didier Raoult, a microbiologist at the University of the Mediterranean in Marseilles, France, successfully recovered Y. pestis DNA from the teeth of a child and two adults dug up from a fourteenth-century mass burial site in Montpellier. The team identified the bacterium using a sensitive technique called the polymerase chain reaction (PCR) to amplify a portion of a gene from Y. pestis called pla. Proving that the Y. pestis was the bacterium during the plague outbreaks.

Hendrik Poinar, a palaeogeneticist at McMaster University in Hamilton, Canada, who co-led the sequencing efforts, considered drilling into teeth and bones to find Y. pestis DNA but wasn’t satisfied with the available detection tools, which were based on PCR. Next-generation DNA sequencers (machines that read short amounts of DNA) could sequence DNA that had been damaged, spending hundreds of years underground. The sequencers allowed Svante Pääbo, a palaeogeneticist at the Max Planck Institute for Evolutionary Anthropology, and his team to sequence a draft of the Neanderthal genome. However, finding and sequencing ancient pathogens in a human skeleton was extremely difficult. Pääbo and his team developed a technique called targeted capture. Using lab-synthesized DNA, it isolated ancient DNA strands from a bone sample, leaving soil microbes and other sequences behind.

In an experiment published in August of this year, Krause and Poinar’s team used sequences from a contemporary plague strain to find and isolate Y. pestis DNA from the teeth of the buried victims. They then sequenced a short loop of DNA called the pPCP1 plasmid (the plasmid partially responsible for bubonic plague infection in humans).

Their results have convinced most scientists that the bubonic Plague was involved in the Black Death. In their most recent paper1, Poinar and Krause completed the ancient genome and showed that it sits at the root of an evolutionary tree that comprises 17 contemporary strains of Y. pestis. This indicates that the Black Death strain spawned many of the forms of Y. pestis that infect humans today.


Y. pestis seemed to have changed very little over the past 660 years. The genome of the Black Death strain differs from the modern Y. pestis, but each genetic difference is found in at least one contemporary strain. These results contradict the findings of Pionar and Krause as there is no evidence for why the bacterium could suddenly create such a massive outbreak as the Black Death. The team is now looking for other genetic changes that could account for the ferocity of the Black Death, such as rearrangements in the genomes.


  1. “The Great Mortality: An Intimate History of the Black Death, the Most Devastating Plague of All Time” by John Kelly
  2. “The Black Death: Natural and Human Disaster in Medieval Europe” by Robert S. Gottfried
  3. “The Plague: The Extraordinary Story of a Singular Disease” by Wendy Orent
  4. “The Black Death and the Transformation of the West” by David Herlihy
  5. “The Coming Plague: Newly Emerging Diseases in a World Out of Balance” by Laurie Garrett
  6. “Plagues and Peoples” by William H. McNeill

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Unlocking the Secrets of the Black Death: Mysteries of Yersinia Pestis. (2023, Aug 29). Retrieved from https://edusson.com/examples/unlocking-the-secrets-of-the-black-death-mysteries-of-yersinia-pestis

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