Scientific Facts about the Black Death

By Lucie Laumonier

Recent years have seen much research into the plague, helping us better understand how this pandemic came about and spread across the medieval world. Here are nine scientific facts about the Black Death, ranging from when it started to the role of animals. 

Plague history has been profoundly renewed these past twenty years by the recovery of aDNA (ancient DNA) of Yersinia pestis in medieval human remains, the sequencing of the bacteria’s genome, and the establishment of its phylogenetic tree (e.g. its genealogical tree).


A pandemic is defined as an epidemic disease that spreads across continents. The first plague pandemic known to historians occurred in the sixth and seventh century and is usually dubbed the “Justinianic Plague,” after the Byzantine emperor Justinian. The Black Death is the second known plague pandemic. The third pandemic began in the nineteenth century and reached the entire globe. However, it is likely that the Justinianic plague was not the first outburst of Yersinia pestis. Plague may have been responsible for suggested population declines in the Bronze Age, in the fourth millennium BCE and early third millennium BCE.

1. Plague Skeptics and Plague Deniers Were Wrong: Plague is Plague

The plague is a disease coming from a bacterium known as Yersinia pestis. The bacterium is named for the Swiss-French bacteriologist Alexandre Yersin who identified the pathogen in the midst of the third pandemic, in Hong Kong, in 1894. But, even if the bacterium responsible for the third pandemic had been identified in the nineteenth century, no scientific hard proof existed before the early 2000s to assert with certainty that the Black Death and Justinianic plague had been caused by Y. pestis. Most historians believed that Y. pestis was responsible for the first and fecond pandemics, but at the time it was only in the realm of hypothesis.


In 1984, British zoologist Graham Twigg published The Black Death: A Biological Reappraisal, in which he contended that the Black Death was, in fact, anthrax. His works inspired others. British sociologist Susan Scott and biologist Christopher J. Duncan argued in their 2001 book, Biology of Plagues, that ebola was actually responsible for the second pandemic. Then, in 2002, Samuel K. Cohn, a professor of medieval history at the University of Glasgow, published a rather controversial article, ‘The Black Death: End of a Paradigm’ in The American Historical Review and an even more controversial book The Black Death Transformed. Cohn was certain that the Black Death had not been caused by Y. pestis but was unsure about the nature of the illness, which he called ‘Disease X’.

Twigg, Scott, Duncan and Cohn based their reasoning on a variety of arguments. Among these, the fact that mass death of rats, attested during the third pandemic, had not occurred in medieval Europe; the pace at which the nineteenth-century plague had spread vs. the speed of spread in the medieval and early modern eras; some discrepancies in symptoms between the three pandemics; variations in climate and environment in plague foci – to only cite a few.

Science soon proved plague skeptics wrong. In the early 2000s, a team of archeologists and microbiologists excavated a plague cemetery in Marseille, France and were able to extract Y. pestis’ DNA from a human body. This astonishing discovery proved that the plague was indeed plague, at least in the fourteenth century. Research continued across Europe while techniques and methods to identify Y. pestis in ancient corpses greatly improved. A wide array of cemeteries have since yielded hard evidence of plague both for the Justinianic plague (sixth and seventh centuries) and the second pandemic (thirteenth to eighteenth century).

It is of course possible that some of the epidemics attested in the medieval and early modern eras and described as being a ‘pestilence’ in written documents were not plague. But Y. pestis is, with absolute certainty, the cause of the first wave of the Black Death (in Europe, from c. 1347 to 1351), as well as the pathogen responsible for the first pandemic. The issue is that historian Samuel K. Cohn was very reluctant to acknowledge the paradigmatic change and resisted the scientific proof for a rather long time. If he now seems to have come to terms with the fact that the second pandemic was indeed the plague, his 2000s works and publications should not be used as solid secondary sources about the Black Death.


2. Yersinia Pestis has a Genealogical Tree

The sequencing of the Y. pestis genome has enabled microbiologists to track down the bacterium’s mutations and branches. When tracking down changes in Y. pestis’ genome, microbiologists can draft a genealogical tree of the disease, going back to its Bronze Age ancestor. The plague, like the flu, is capable of evolving: it branches out, and the branches are “strains” or “variants” of the disease. You are probably familiar with the notion of strains because of the numerous variants of COVID-19! The plague therefore has what is called a phylogenetic tree–a genealogical tree–with a common ancestor and branches out in branches, or variants, or strains.

The phylogenetic tree of Y. pestis has invaluable impacts for plague research, in enabling researchers to:

  • date the different plague strains
  • track the plague’s evolution in time (first this strain, then this one)
  • map out the strains’ spread across the globe, based on the location where certain strains of Y. pestis were recovered

In sum, tracking these genomic changes enables researchers to identify where and when epidemics broke out.


The existence of different plague branches explains for instance discrepancies in plague symptoms between the first, two and third pandemics, as well as the different speeds at which plague can spread. In the same way that certain variants of COVID-19 are more contagious than others, certain branches of Y. pestis were and are more virulent than others. When a mutation is successful, plague ‘catches on’ and massively spreads to mammals, humans included.

Yersinia pestis was born some 5,500 years ago (fourth millennium BCE) as a mutation of the bacterium known as Yersinia pseudotuberculosis. This ancestor of medieval and modern plague lacked virulence, could not yet cause bubonic plague (only pneumonic and septicaemic plague) and was not transmissible from fleas to humans. A Russian late Bronze Age burial has recently revealed that, in the second millennium BCE, Y. pestis was capable of causing bubonic plague and could be transmitted to humans by flea bites. These changes probably occurred during the third millennium BCE. Research also shows that prehistoric Yersinia pestis originates probably from Central/East Asia, where natural foci of plague still exist.

From Z. Zhou et al. (2020), ‘The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity’, Genome Research 30, no. 1

3. The Black Death Actually Started in the Thirteenth Century

The story of the Black Death is too often told through Western European lenses, where it arrived in 1347 according to the account of Michele da Piazza:

In October 1347, at about the beginning of the month, twelve Genoese galleys, fleeing from the divine vengeance which Our Lord had sent upon them for their sins, put into the port of Messina. The Genoese carried such a disease in their bodies that if anyone so much as spoke with one of them he was infected with the deadly illness and could not avoid death.


The Genoese galleys in question brought the plague from somewhere. Historians agree that sailors and merchants caught the plague in the Black Sea c. 1346. The circumstances are unclear, but they probably came into contact with Yersinia pestis through rodents hidden in bags of grain in the city of Tana, rather than from the theoretical and unverified story of bodies catapulted by Mongol armies in Caffa. Historical accounts confirm that the Mongols of the Golden Horde were carriers of plague at least fifteen years before its transmission to the Genoese, pointing in the direction of a Central Asian origin of the plague.

What happened in Central Asia, then? This is where science sheds light on the early years of the Black Death. Scientists and geneticists have shown that, prior to the fourteenth century, Yersinia pestis evolved into four different branches and began to spread. This event is dubbed “The Big Bang” by microbiologists. Each branch then mutated independently from each other to adapt to their hosts, the climate, etc. The strain of the Black Death found in England in the fourteenth century, for instance, had mutated twice since the Central Asian ‘Big Bang’ and carried slightly different properties.

The ‘Big Bang’ occurred probably in the thirteenth century and was gradually spread by Mongol armies. Yersinia pestis evolved when coming into contact with new hosts and new environments, while plague reservoirs were created in the wild and became endemic into the local rodent populations–which would then transmit it to humans. Monica Green convincingly argues that the plague was circulating in the thirteenth century as far as in Iran and Iraq, but created smaller outbreaks that are unevenly recorded in written sources.

4. Mass Graves or No Mass Graves?

When trying to imagine life during the Black Death, we are prone to think about bodies piling up in the streets, transported in carts and hastily dropped in large mass graves. There is indeed evidence of mass burials during medieval episodes of plague. In 2020, 48 bodies were recovered from Thornton Abbey, England, likely connected to the deadly disease. The mass burial includes the remains of 27 children and of 21 adults, men and women. But, as surprising as it might be, emergency burials in pits or mass graves were actually not that common in the Middle Ages.

“Despite the fact it is now estimated that up to half the population of England perished during the Black Death, multiple graves associated with the event are extremely rare in this country, and it seems local communities continued to dispose of their loved ones in as ordinary a way as possible,” says Dr. Hugh Willmott, an archaeologist from the University of Sheffield, who has been working on the Thornton Abbey site for a decade. In fact, the rarity of mass graves during the second pandemic is not limited to England.

Indeed, a comparative analysis of some 20 European cemeteries – from France mainly – shows that the plague dead were buried following traditional usages and practices, even if more hastily. Bodies were covered in a shroud and, in some instances, placed into caskets. In some communities, when the parish cemetery overflowed with bodies, specific burial grounds were created. But even there, few multiple burials are attested. In Montpellier, a southern French city that counted over 30,000 inhabitants on the eve of the Black Death, archeologists have studied the St. Come and St. Damien cemetery. They found DNA evidence of the presence of Yersinia Pestis, but no mass grave. In one instance, a child had been buried with two adults, a man and a woman, assumedly his parents.

In Western Europe, the vast majority of Black Death victims were buried according to the ordinary usages.

5. Not everyone was equally at risk of dying

Bioarchaeology is a rich field of study at the crossroads of history and anthropology that has been gaining momentum the past decade. Bioarchaeologists study the remains of people dead for centuries to better understand how they lived and why they died. When looking at bodies excavated from medieval cemeteries, they assess their gender, their age, the traumas they’ve been through. In some instances, they are able to assess their food regimen and can extrapolate on their social status. Research is particularly developed in England. The current section is therefore based on evidence recovered from English sites.

Recounting the Black Death of 1348-1349, most medieval chroniclers claimed that the disease was indiscriminate and killed people of all conditions, age and gender. But, Boccaccio’s Decameron tells the tales shared by seven young and wealthy protagonists who had fled the plague in Florence and sought refuge in a secluded countryside villa. If the rich had the means to protect themselves from the ravages of plague by leaving large urban centers, the poor had not. They lived in densely populated neighborhoods with low hygiene. Moreover, humble and poor people suffered from rampant malnutrition; their bodies were exhausted by long and tiresome hours of physical work. They were more prone to developing diseases than the wealthy, and had fewer chances of surviving illness.

The poor, in sum, were more at risk of dying from plague episodes than the wealthy. Evidence from bodies recovered in medieval cemeteries indeed show a higher prevalence of death among people exhibiting signs of malnutrition and prior diseases and/or traumas. Textual sources confirm these findings. Royal genealogies and inquisitions post-mortem for well-off tenants in chief show that the higher nobility had a mortality rate of 4.5% in 1348 and 13% in 1349. Well-off landowners died at a rate of 27%. Landless men showed mortality rated anywhere between 40% and 100% in some unfortunate manors.

6. The Black Death Lasted until the Eighteenth or Nineteenth Century

We tend to associate the Black Death with the epidemic that reached Europe in 1347 and lasted until the early 1350s. However, if the plague went dormant for approximately a decade, dozens of flare-ups are attested in historical records. In his Historica Anglicana, Thomas Walsingham describes the fourth pestilence that devastated Great Britain:

In 1375 the weather was scorching, and there was a great pestilence which raged so strongly in England and elsewhere that infinite numbers of men and women were devoured by sudden death. […] In the summer of 1379, due to a hostile configuration of the planets, plague broke out in the north country on a scale never seen before. The mortality waxed so powerful that almost the whole region was rapidly stripped of its best men; and among the middle classes it was said that nearly every house was deprived of its residents and left standing empty. Even large families were wiped out by the plague, with not one person left alive.

Plague had become endemic in Western Europe and in the Middle East and caused frequent outbreaks, to the point where plague historians and scientists consider that the Black Death only went extinct in the eighteenth century in Europe. Three eighteenth-century outbreaks symbolize the end of the second pandemic: the 1720-22 plague of Marseille, France, that would have killed as many as 100,000 people in the area; the 1743 outbreak of Messina, Sicily with estimated fatalities of around 40,000 people; and the 1770-72 plague of Moscow, Russia, which would have claimed a bare minimum of 50,000 lives, maybe up to 100,000.

In the Ottoman Empire, however, the second pandemic probably lasted to the nineteenth century and may have overlapped with the third pandemic, dubbed ‘The plague of Hong Kong.’ The endemic nature of Yersinia Pestis in the Middle East contrasts with the situation of Europe at the time, where, in the eighteenth century, only sporadic outbreaks – even if claiming tens of thousands of lives – were attested. Eighteenth-century European public authorities and scientists therefore developed a long-standing narrative holding that the plague was imported to Europe from the Ottoman Empire.

Not only this narrative had no scientific ground (plague reservoirs existed in Europe) but it was harmful to Western representations of the Ottoman Empire. It participated in European colonial views according to which plague flowed from “less civilized” places to “centers of civilization.” As Nükhet Varlık argues, “Colonial anxieties thus found a scientific justification in this emphasis on the disease’s place of origin […] and that their contagion could affect civilized peoples and places.” Other diseases which impacted Europeans, such as syphilis, were described as having foreign origins. In Western thought, evil illnesses could not come from within the community but were brought in by the outside.

7. Your cat (and medieval cats) could be plague-carriers

It’s not a joke, unfortunately. On Sept. 1, 2022, the Wyoming Department of Health reported that a cat had just died of plague. In 2021, plague had been detected in six Colorado counties and may have caused the death of a 10-year-old child. There too a cat had tested positive for plague.

But cats are not the only ones to blame. Plague is naturally present in the wild in what scientists call “plague foci” or “plague reservoirs.” Central Asia and the United States are among the most active plague reservoirs today. In Colorado, plague is present in squirrels, woodrats, chipmunks and prairie dogs. Recent research suggests that, across the world, as many as 351 mammal species are susceptible to carrying Y. pestis (thus not counting arthropods, such as fleas). Among these 351 mammal species, close to 50 act as primary plague hosts. It means that they are the primary vectors of plague. Almost half of them (22 to be exact) are actually immune to the disease: they carry Y. pestis but won’t die from it.

The vast majority of these primary plague hosts are rodents. Humans and other mammals coming into contact with plague-ridden rodents are at risk of contracting the disease. Research conducted by the National Wildlife Research Center in the United States between 2005 and 2018 on tens of thousands of wild mammals found that 11% of sampled black-tail prairie dogs tested positive to plague antibodies, meaning that they had contracted the plague at some point.

Primary plague hosts, such as rats or marmots, transmit Y. pestis to other mammals through parasitic arthropods (fleas jumping from one animal to the other) or when eaten by predators, such as cats or coyotes. In the above-mentioned research of the US National Wildlife Research Center, 9% of the coyotes sampled had been in contact with plague, and as many as 14% grey wolves also tested positive to plague antibodies. How is this relevant to the history of the Black Death? Well, simply by shedding light on the fact that a wide array of mammals could have acted as vectors of transmission, and not just rats.

8. Medieval Rats Were not the Sole Culprits

One of the reasons why plague skeptics doubted that the Black Death was indeed plague was because of the absence of reports of rats’ dies-off during the second pandemic, while, during the third, scientists had observed mass deaths of rats. Turns out, rats rarely die out in the open. Plague skeptics also argued that the plague’s range and the black rat’s range did not correspond, hence that plague could not have reached certain areas in which rats were absent. It is however established, now, that as many as 47 different mammal species are primary plague hosts, that they can transmit Y. pestis to a larger number of animals (humans included), with 351 species that are known, to date, for potentially carrying plague. The black rat, therefore, was not the only animal spreading the plague during the second pandemic.

Rather interestingly, some mass deaths of animals were actually reported during the second pandemic! Byzantine author Nicephorus Gregoras, who died in 1360, indeed reported about the death of mammals, and mentions rats:

The calamity did not destroy men only, but many animals living with and domesticated by men. I speak of dogs and horses and all the species of birds, even the rats that happened to live within the walls of the houses. The prominent signs of this disease, signs indicating early death, were tumorous outgrowths at the roots of thighs and arms and simultaneously bleeding ulcerations, which, sometimes the same day, carried the infected rapidly out of this present life, sitting or walking.

Besides rats, what animals could transmit plague to humans? In North Africa and the Middle East, a species of gerbils acts as plague carriers. They can notably transmit the disease, through the proxy of fleas, to camels. These gerbils probably roamed around caravans and relay posts and could have infected camels, domesticated and widely used by medieval populations for transport.

In Central Asia, marmots are among the primary plague hosts. They were a food of choice for the medieval Mongols, who harvested them for meat and pelts. In the Ottoman Empire, white storks were seen as omens of plague. Recent research shows they can carry plague-infested fleas. In the Ottoman Empire, the trajectory of their migratory routes actually matched the spread of plague. In the alpine regions of Western Europe, marmots could have played the role of primary plague hosts.

In sum, a wide array of animals were and are involved in spreading Y. pestis, from commensal animals, which live in close quarters with humans, to wild animals. Ruminant animals and predators do not act as primary plague hosts, but catch the bacterium from rodents (through their fleas or by eating them) explaining why, from cats to camels, the plague is still present today across the globe. Crucially, the existence of plague reservoirs and the capacity of Y. pestis to be carried by over 350 species of mammals – not counting birds and arthropods – explain its spread and wide range in the medieval world. The role of fleas in cross-species contamination is the last section of this article.

9. How Fleas Transmit Plague

“Fleas are born in warm, moist dirt, especially if the body heat and breath of animals is admixed with the dirt,” describes Albertus Magnus in his thirteenth-century treatise De Animalibus. He continues:

The flea is a dark, round creature with a very sharp proboscis that it uses to penetrate the pelts of animals and draw blood […]. It has spearlike hindlegs for leaping and six other legs for walking. Despite the minuscule size of its body, it moves at a rapid pace. Its head is rather pointed; it imbibes so much blood that it discharges a constant flow of fecal material like dried, blackened blood from its hind end. Its eggs resemble the nits of lice, and now and then the female is found to be laden with them.

Full disclosure, fleas have only six legs! Let me explain how fleas can transmit Yersinia pestis to their hosts. When a flea bites an infected host, the bacteria is sucked in with the blood. Chemical cues in the fleas’ stomach tell the bacteria it’s in a flea now. At this point, it goes into a reproductive frenzy, creating this mass of bacteria and organic material called a biofilm that eventually blocks the flea’s esophagus. When the flea hops onto another host to grab a meal, it cannot swallow the blood, and so regurgitates it back into the host along with Yersinia pestis cells. The new host is now infected.

Fleas travelled on living animals, on humans, as well as on pelts that were sold and purchased. They were also endemic in medieval houses, and medieval authors were well aware of that. To get rid of them they had designed a wide range of remedies. The Byzantine treatise Geoponika reads:

Dig a hole; grind oleander leaves and place in it; they will all gather there. Otherwise, soak the floor repeatedly with amorge; then grind wild cumin and mix with waters, and grind 10 drams of squirting cucumber seed and add to the water; sprinkle this in the room and you will make the fleas split.

In De Animalibus, Albertus Magnus quotes a recipe coming from Avicenna:

Fleas can be put to rout by sprinkling the house with an infusion of colocynth which causes them to leap for safety and vacate the premises; the same results can be achieved with a decoction of blackberries.

He adds:

Some writers have contended that when the blood of a goat is poured into a crevice of an indoor room, fleas flock to the spot and die; similarly, they are lured together on a piece of wood smeared with hedgehog fat.

If you cannot put your hand on hedgehog fat, modern-day flea repellants should do the trick.

And, if you are a flea specialist, you know that most flea species are specialized for one or a few species of mammals. There are human fleas (named pulex irritans for obvious reasons) and cat fleas, dog fleas, rat fleas etc. But fleas can adapt to a variety of hosts. While a cat flea might prefer to hang out on cats, they can survive and bite a dog or a human. Which is how the disease gets from one animal species to the other, and ends up infecting humans. Now, you know everything about medieval fleas and their role in transmitting plague!

Lucie Laumonier is an Affiliate assistant professor at Concordia University. Click here to view her page or follow her on Instagram at The French Medievalist.

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Further Reading:

Hannah Barker, ‘Laying the Corpses to Rest: Grain, Embargoes, and Yersinia pestis in the Black Sea, 1346–48’, Speculum 96, no 1 (2021): 97-126.

Ann Carmichael, ‘Plague Persistence in Western Europe: A Hypothesis’, The Medieval Globe 1 (2014): 157–92.

Yujun Cui et al., ‘Historical Variations in Mutation Rate in an Epidemic Pathogen, Yersinia Pestis’, Proceedings of the National Academy of Sciences 110, no. 2 (2013): 577–82,

Sharon N. DeWitte and Maryanne Kowaleski, ‘Black Death Bodies’, Fragments 6 (2017): 1–37.

Sharon N. DeWitte, ‘Stress, Sex, and Plague: Patterns of Developmental Stress and Survival in Pre- and Post-Black Death London’, American Journal of Human Biology 30, no. 1 (2018): e23073.

Monica H. Green, ‘The Four Black Deaths,’ The American Historical Review 125, no. 5 (2020): 1601-1631.

Lester K. Little, ‘Plague Historians in Lab Coats’, Past & Present 213, no. 1 (2011): 267-290.

Ahmad Mahmoudi et al., ‘Plague Reservoir Species throughout the World’, Integrative Zoology 15 (2020): 1–14.

Simon Rasmussen Morten, Erik Allentoft, Kasper Nielsen et al., ‘Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago,’ Cell, vol. 163-3 (2015): 571-582.

Paul Slack, ‘Perceptions of Plague in Eighteenth-Century Europe’, The Economic History Review 75, no. 1 (2022): 138-156.

Maria A. Spyrou et al., ‘Analysis of 3800-Year-Old Yersinia Pestis Genomes Suggests Bronze Age Origin for Bubonic Plague’, Nature Communications 9, no. 1 (2018): 2234

Nükhet Varlık, Plague and Empire in the Early Modern Mediterranean World: The Ottoman Experience, 1347–1600 (Cambridge: Cambridge University Press, 2015).

Nükhet Varlık, “New Science and Old Sources: Why the Ottoman Experience of Plague Matters,” The Medieval Globe 1, no. 1 (2015): 193‑227.