When Europeans arrived in the New World, they carried with them microscopic, deadly organisms… like smallpox, measles and flu… which caused devastating outbreaks among the indigenous people.

One of those outbreaks was what became called the cocoliztli epidemic of 1545, among the people known as the Mixtecs, in what is today southern Mexico. The victims suffered rashes and fevers; blood streamed from their eyes, noses and mouths. Millions died. But we're still not sure what caused it.

So scientists looked to 10 victims, buried in communal graves in one of the afflicted towns, for clues. They sequenced DNA from within their pulpy tooth cavities. Most studies of ancient bones ditch all the associated microbial DNA, so that only the host’s DNA is analyzed. But in this case the bacterial and viral DNA were the stars of the show. Which also meant a lot more genetic data to sift through.

"The difference is the needle in the haystack." Noreen Tuross, a biochemist at Harvard University. "This is a much bigger haystack."

Using a new algorithm to help them dive into that huge haystack, they found a needle: genetic evidence of the deadly Salmonella enterica Paratyphi C bacterium, which causes enteric fever.

The results are in the journal Nature Ecology & Evolution. [Åshild J. Vågene et al., Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico]

The researchers stopped short of pinning the epidemic on the salmonella alone. "Could there have been other organisms around? Yes. We didn't find them. How do you know that what you didn't find isn't there? That's ridiculous."

And it's uncertain the disease had European origins—though there is evidence it existed in Norway, three hundred years before Columbus sailed. But this effort arms archaeologists with a new tool to study not just great civilizations…but also the world of microbes with which they coexisted.

—Christopher Intagliata

[The above text is a transcript of this podcast.]