Microbes in an ancient mummy
Posted on February 1, 2016 by Anand Jagatia
Last month, researchers announced the discovery of ancient gut microbes in the frozen remains of a prehistoric mummy. DNA recovered from the bacterium, Helicobacter pylori, may ultimately change the way we think about the migration of our species. We spoke to study author and microbiologist Dr Frank Maixner about the significance of this new research.
A 5,300-year-old mummy is probably the last thing you expect to find when you’re out hiking in the Alps. But that’s exactly what happened to two mountaineers in 1991 when they stumbled across the body of Ötzi the “Iceman”. Buried for millennia under snow and ice, with his tissues, organs and even his clothes almost perfectly preserved, the Iceman has given researchers an incredibly rare opportunity to look deep into the past.
Since he was found, scientists have been able to piece together a huge amount about the Iceman’s life. He had healed fractures, 61 tattoos, and his DNA shows he had brown eyes. As for his death, in all likelihood he was murdered by the arrow which was found lodged in his back. Scientists think this probably happened in late spring or summer, based on the variety of pollen residues found in his intestine.
This latest discovery about the Iceman’s gut bacteria was made while researchers were trying to reconstruct his diet using the contents of his mummified stomach. For a long time, scientists were unable to even find Ötzi’s stomach because it had moved during the mummification process. But in 2009 it was spotted on an old radiographic image, and a new sampling campaign began.
The Iceman is normally kept under conditions similar to those found in the glacier – at -6 degrees C and under high humidity. In light of the new discovery, the mummy was removed from storage for a brief time so that new samples could be taken. Using an incision from a previous campaign, the team gained access to the stomach contents and the stomach wall.
“It was a very interesting experience,” says Frank. “People gathered from many different backgrounds – we had a gastroenterologist performing the endoscopy. He’s had a lot of experience with modern patients, but sampling a mummy was definitely new for him.”
Because Ötzi is such a rare and valuable resource, great care was taken during the preparation and sampling, which took two whole days. “It’s a balance between obtaining the most important material while harming the mummy as little as possible,” Frank explains. “This is not always easy, but modern molecular techniques enable us to keep the sample sizes very small – we don’t need much to extract DNA.”
Looking at the DNA of the animal fibres found inside the stomach, Frank and his colleagues deduced the Iceman’s last meal was an Alpine ibex. But in the midst of this stomach DNA sample, they also found a trace of one of the Iceman’s original gut microbes: Helicobacter pylori.
H. pylori is a species that has accompanied humankind for about 100,000 years. It’s transmitted from parent to offspring, and between children who have close physical contact. This means that different populations of humans carry their own distinct Helicobacter strains. When populations mix and breed, the genomes of their Helicobacterstrains also start to combine, and so the DNA of H. pylori can be used to infer the movements of its host’s ancestors.
Before the team could start analysing the Helicobacter genome, they had to confirm that it really was ancient DNA, rather than from contamination or post-mortem bacteria. This is no easy task, but in the last few years, developments in the field have made ancient DNA analysis much more reliable.
As DNA degrades over time, one of its four building blocks (cytosine, C) loses a chemical group, which converts it into another (uracil, U). This “C to U conversion” is proportional to the age of the DNA, and how well it is preserved. “The older the sample, the more converted bases we see after sequencing compared to the modern reference genome, especially at the ends of the DNA which are more exposed,” says Frank. “This gave us proof that the DNA was really ancient.”
Reconstructing the H. pylori genome, the team found something rather unexpected. Modern Europeans harbour a hybrid strain of Helicobacter that contains a mixture of ancient African and Asian components, reflecting the fact that these two populations mixed at some point in the past.
This is something the researchers predicted they would also see in the Iceman – but instead they found an almost “pure” ancestral Asian strain, without the African component. If the Iceman is representative of his time, this implies that the arrival of the African H. pyloripopulation to Europe must have happened after he died, which is much later than previously thought.
“We truly believe that the introduction of the so-called African component happened after the Iceman’s time,” says Frank. “So the recombination event which led to the modern H. pylori strain occurred in a quite short time frame, within the last 5,000 years.”
Of course, this analysis is based on just one sample, so it’s difficult to draw conclusions about entire populations living at that time.
“It’s hard to say we can claim he really reflects the population of the whole of Europe,” Frank admits. “But we can say from modern rural studies that there is a high transmission rate of H. pylori between people, especially because of hygiene conditions. So there is a high probability that others around him also carried this strain.”
It’s also possible to rule out the idea that the Iceman travelled from Asia and brought his Helicobacter with him, because analysis of the isotopes in his bones and teeth show he was born and lived in the valleys where he was found.
It’s unlikely that we will find any more mummies that are as well preserved as the Iceman. But in the future, scientists may be able to expand on these results by looking elsewhere, such as coprolites (fossilised faeces) and dental calculus, which is a second layer of calcium sometimes found on the teeth of recovered skeletons. Dental calculus is usually rich in mouth flora, and it’s possible that scientists will find H. pylori on some specimens.
“These are things that will be much more challenging than [analysing] the Iceman was already,” says Frank. “But who knows? Five years ago, we wouldn’t have even predicted to find this much, so I’m confident.”