T

he bodies were discovered accidentally.

While digging sewers for a suburban development outside Munich, Germany, construction workers saw what looked like bones. Turns out it wasn’t a single corpse. There were huge clusters of them, stretching underneath gardens and roads — 1,451 to be exact. The archeologists and boy scouts who later excavated had no way of knowing that these corpses would help scientists understand one of the deadliest diseases on earth.

That disease is plague. And a paper published Tuesday, 51 years after those skeletons were first discovered, provides a detailed analysis of the bacterial DNA responsible for filling that ancient graveyard at Altenerding — and for killing a third to a half of the population of the known world at the end of the Roman Empire.

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The finding isn’t just a historical curiosity. It’s a tool for advancing biomedical science.

These ancient bits of DNA form a kind of evolutionary archive, telling the story of a relatively harmless stomach bug that became a rampant killer. Researchers hope to use that story to look for similar transformations in today’s bacteria, and to help us prepare for future outbreaks — both of plague and of other pathogens.

The corpses at Altenerding died in the the first known plague pandemic, which started around 541, centuries before the Black Death that swept through Europe in the Middle Ages. People would develop a fever, along with swellings in their groins or under their arms. They would be dead three days later.

“The Roman emperor Justinian, ruling in Constantinople, ordered an imperial official to count the bodies going out of the gates, and there were so many that they just gave up,” said Michael McCormick, a Harvard historian who studies the Justinianic plague, and one of the authors of the paper. “They gave up around 230,000.”

Most people assume plague disappeared along with the Middle Ages, but it’s still very much alive. Hundreds of patients in Madagascar get bubonic plague every year, and there are scattered infections elsewhere in Africa, in Asia, and in the Americas, too. Last year, at least 15 cases were reported in the United States, mostly transmitted by fleas that had fed on prairie dogs and other wild rodents out West.

To find and analyze 21st century plague samples, researchers need look no farther than rats in Madagascar, or ground squirrels in Arizona.

But ancient samples are trickier to come by.

Plague remains
Excavation of the Altenerding cemetery during a visit by a delegation of the district of Upper-Bavaria in the year 1967. Museum Erding

Scientists hadn’t even thought to look for plague in the bodies exhumed from Altenerding until 2014, when another team published results from a similar cemetery about 20 miles away. That one was a bit more obvious, because five or six bodies had been dumped in a single hole, suggesting some kind of fast-spreading infectious disease.

The earlier paper provided more evidence that Justinian’s pandemic was indeed the same disease as the Black Death. But scientists wondered if they could get an even better DNA sample from Altenerding.

So they went into Munich’s State Collection of Anthropology and Paleoanatomy and started pulling teeth.

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“It turns out with a blood-borne pathogen like plague, the teeth tend to be a pretty good time capsule for DNA,” explained David Wagner, a biologist at Northern Arizona University, and the author of the 2014 paper. “In the underside of your teeth, there are a lot of blood vessels that feed the dental pulp.”

But like cookies kept in a pantry for too long, DNA begins to crumble over time — and finding 1,500-year-old plague is a crapshoot.

“Even if you have two teeth from the same individual, you’re not necessarily going to get the DNA from both teeth,” said Michal Feldman, a researcher at the Max Planck Institute for the Science of Human History, and one of the authors of the new paper.

Only two of 20 skeletons studied yielded reliable plague DNA, and only one of them had enough for analysis.

But the researchers were determined: With a drill, they extracted a fine bone dust, and filtered out anything that wasn’t DNA. Then, using a bit of contemporary plague as a kind of magnet, they dragged out the disease’s genetic material, leaving behind the dead woman’s own DNA and 15 centuries worth of biological contaminants.

It wasn’t much, but it was enough to sequence, and the results were more detailed than what was found in 2014. The team found some 30 spots on the genome that were different from other strains of plague.

None of those bits of DNA alone can explain why, 5,000 years ago, bacteria that caused little more than stomach upset evolved into the terrifying scourge that is Yersinia pestis. Nor can they tell us exactly what caused each plague pandemic to arise and then to recede.

But this kind of study “allows us to make a time line of the important genes,” said Wyndham Lathem, a plague researcher at Northwestern.

Some of these genes may have been acquired from other bacteria, because microbes make a habit of sidling up to each other and exchanging genetic material through temporary openings in their membranes. This kind of behavior is taking place all the time — and that’s how the first antibiotic resistance may have arisen in plague in the 1990s. That means that certain traits — like virulence or resistance — could potentially be passed from one species to another.

And so learning about how these evolve in one kind of bacteria could have much broader implications.

“Understanding what happened during history, understanding when plague emerged, and how it transformed — that is very interesting from a basic point of view,” said Elisabeth Carniel, a plague researcher at the Institut Pasteur in Paris “But also it shows that these kind of events can occur again at any time, anywhere in the word. Understanding how it happened in pestis might be useful to be prepared in case of other types of outbreaks.”

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