Bodies, Bacteria and a 500-Year-Old Gallstone

The bacteria in and around us are generally harmless... until they aren't. A 16th century genome has some clues as to how and why it happens.


Most strains of E. coli are always with us, and most of the time they are perfectly harmless. They live inside our intestines, starting shortly after birth, and usually cause us no symptoms at all.

This ever-present and harmless behaviour earns them a special name — commensals — but they can become dangerous during periods of stress, disease, imbalance, or immunodeficiency.

For the first time, a centuries-old E. coli genome has been reconstructed from remnants found in the gallstone of a 16th century mummy. This information is shedding new light on how these bacteria evolved.

The research comes from an international team led by researchers at McMaster University. Their study was published in Communications Biology.

When most people think of how bacteria can cause disease, they think of infections: germs invade the body, and as they multiply they cause damage and illness.

By contrast, commensals enter the body without causing symptoms and they wait for a future opportunity to strike. E. coli strains remain a major public health concern, but little is known about their evolutionary history, or even how many deaths they may have caused.

“A strict focus on pandemic-causing pathogens as the sole narrative of mass mortality in our past misses the large burden that stems from opportunistic commensals driven by the stress of lives lived,” said principal investigator Hendrik Poinar, professor of anthropology and Director of McMaster’s Ancient DNA Centre, in a press release.

Despite their importance, commensals are particularly hard to study because they are everywhere. Every person, alive or dead, is colonized by them.

In life, the gallbladder is normally sterile. Gallstones can form if bacteria make their way in, solidifying and capturing the contents like a time capsule. This is what happened in the 16th century Italian noble whose remains were used in the study.

Still, reconstructing the ancient E. coli genome was far from easy. The DNA was badly degraded over time, and contaminated by modern day strains in the surrounding environment. The team had to isolate the authentic genetic material and piece it back together.

With the reconstructed genome in hand, the team was able to compare it to today’s strains. This analysis revealed how genes had changed over the centuries. Finding a close genetic match to a living strain, they found that it was likely a commensal.

In truth, bacteria occupy positions along a continuum from commensals that are almost always harmless, to obligatory pathogens that always cause disease when present. Where exactly one lands can change as genes are acquired, lost, or mutated. Having these data will help researchers understand the history of these shifts, including understanding how E. coli strains may have developed antibiotic resistance or become more likely to cause food poisoning.

These insights mean that this ancient genome still has relevance today, and hopefully that will translate into better care for patients as our understanding evolves.

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Karyn Ho is a science animator and engineer who thrives at the interface between science, engineering, medicine, and art. She earned her MScBMC (biomedical communications) and PhD (chemical engineering and biomedical engineering) at the University of Toronto. Karyn is passionate about using cutting edge discoveries to create dynamic stories as a way of supporting innovation, collaboration, education, and informed decision making. By translating knowledge into narratives, her vision is to captivate people, spark their curiosity, and motivate them to share what they learned.