Thousands of years ago, across the Eastern Mediterranean, multiple Bronze Age civilizations took a distinct turn for the worse at around the same time.

The Old Kingdom of Egypt and the Akkadian Empire both collapsed, and there was a widespread societal crisis across the Ancient Near East and the Aegean, manifesting as declining populations, destruction, reduced trade, and significant cultural changes.

As usual, fingers have been pointed at climate change and shifting allegiances. But scientists have just found a new culprit in some old bones.

In remains excavated from an ancient burial site on Crete, in a cave called Hagios Charalambos, a team led by archaeogeneticist Gunnar Neumann of the Max Planck Institute for Evolutionary Anthropology in Germany found genetic evidence of bacteria responsible for two of history's most significant diseases – typhoid fever and plague.

Therefore, the researchers said, widespread illnesses caused by these pathogens cannot be discounted as a contributing factor in the societal changes so widespread around 2200 to 2000 BCE.

"The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete," they wrote in their paper, "emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and beyond."

Yersinia pestis is a bacterium responsible for tens of millions of deaths, most occurring in the course of three devastating global pandemics. Catastrophic as this disease was in centuries gone by, its impact prior to the Plague of Justinian, which started in 541 CE, has been difficult to gauge.

Recent technological and scientific advances, particularly the recovery and sequencing of ancient DNA from old bones, are revealing some of that lost history.

We now suspect, for example, that the bacterium has been infecting people since at least the Neolithic period.

Last year, scientists revealed that a Stone Age hunter-gatherer likely died of plague thousands of years before we had evidence of the disease reaching epidemic proportions.

However, the genomic evidence recovered had so far been from colder regions. Little is known about its impact on ancient societies in warmer climates, such as those in the Eastern Mediterranean, thanks to the degradation of DNA in the higher temperatures.

So Neumann and his team went digging through bones recovered from a site on Crete known for its remarkably cool and stable conditions.

They recovered DNA in teeth from 32 individuals who died between 2290 and 1909 BCE. The genetic data revealed the presence of quite a few common oral bacteria, which was expected.

Less expected was the presence of Y. pestis in two individuals and two Salmonella enterica lineages – a bacterium typically responsible for typhoid fever – in two others. This discovery suggests that both pathogens were present and possibly transmissible in Bronze Age Crete.

But there's a caveat. Each of the lineages discovered is now extinct, making it harder to determine just how their infections might have affected communities.

The lineage of Y. pestis they uncovered probably couldn't be transmitted through fleas – one of the traits that made other lineages of the bacterium so contagious in human populations.

The flea vector carries the bubonic version of the plague; humans become infected when the bacterium enters the lymphatic system via a flea bite. Therefore, the transmission route of this ancient form of the bacterium could be different and cause a different form of plague; pneumonic plague, which is transmitted via aerosols, for example.

The researchers said that the S. enterica lineages also lacked key traits that contribute to severe disease in humans, so the virulence and transmission routes of both pathogens remain unknown.

Nevertheless, the discovery suggests that both pathogens were circulating; in regions of Crete with high population densities, they could have run somewhat rampant.

"While it is unlikely that Y. pestis or S. enterica were the sole culprits responsible for the societal changes observed in the Mediterranean at the end of the 3rd millennium BCE," the researchers wrote in their paper, "we propose that, given the [ancient] DNA evidence presented here, infectious diseases should be considered as an additional contributing factor; possibly in an interplay with climate and migration, which has been previously suggested."

Because diseases like plague and typhoid do not leave traces on bones, they are not frequently noticed in the archaeological record. The team suggests that more detailed genetic screening of more remains from the Eastern Mediterranean could help uncover the extent of the impact these diseases had on the civilizations who lived there.

The research has been published in Current Biology.