Helicobacter pylori genome found in the stomach of a 5300-year-old Ice man

Oetzi the Iceman

Oetzi the Iceman was found in 1991 in the high Oetzal Alps that span Italy and Austria.  He is a mummy who gained popularity in the scientific community because of how well he was preserved and thus the potential to provide a glimpse into Europe’s past (he is thought to be around 5,300 years old, alive in the European Copper Age).  Many studies have examined his diet, health, and genetics, but recently researchers were able to discover identify and examine his stomach and intestines.  Biopsy samples were collected and PCR analysis determined the presence of the gram-negative bacteria Helicobacter pylori. 

H. pylori can be found in about half of the world’s population, and while research has pointed to the harmful effects of this bacterial strain, recent work has supported that the bacteria can in fact protect against some illness such as acid reflux and asthma.  However, extensive characterizing Oetzi Iceman’s H. pylori could also shed light on ancient human migration patterns.  Specifically, modern strains of H. pylori are assigned to distinct populations based on their geographical heritage, originating from either ancestral Asian populations (AE1) or hybrids between North Africa and Europe (AE2). 

Comparative whole genome analysis showed that Oetzi Iceman’s H. pylori genome has highest similarity to three apAsia2 H. pylori genomes from India, and further high-resolution analysis of ancestral motifs revealed a co-ancestral matrix, showing that H. pylori shares ancestry with Indian strains but also with most European strains.  Low levels of H. pylori ancestry was shared with the AE2 ancestry, which was interesting to scientists as it suggests AE2 introgression into Europe after the Copper Age.  This was later than what has been proposed previously by the scientific community.  Ultimately, these findings showed that Oetzi Iceman had H. pylori with strong AE1 genetic Asian origins, suggesting that the AE2 bacteria from African heritage began arriving after the Copper Age of European civilization.  

The gut microbiome of a pre-Columbian Andean mummy looks much different than our own

A photo of the mummy whose microbiome was studied

The study of ancient humans’ microbiomes is a topic of growing interest, because it is believed that these microbiomes more closely resemble native or ‘natural’ microbiomes than the ones we have today.  There have been a few studies on humans’ microbiomes at different periods of history, and another data point was added to the list last week.  Researchers from Italy and California were able to measure the microbiome of a pre-Columbian human (11th century to be exact) that was mummified naturally after he died in the cold, harsh, and high elevations of the Andes Mountains in Chile.  The researchers published their findings in the journal PLoS ONE.

The researchers sequenced the bacteria that were in the mummy’s colon, as well as the mummy’s feces.  Strikingly, around 99% of the bacteria belonged to the Firmicutes genus, mainly dominated by Clostridia, and Turicibacter.  In addition, the human appeared to have many bacteria associated with modern day diseases.  For example the mummy’s microbiome contained Clostridium difficile (the cause of C. difficile infection), Trypansoma cruzi (the cause of Chagas’ disease), and many types of human papilloma virus (HPV).  Finally, the researchers noted that many genes associated with antibiotic resistance were found in the mummy’s microbiome, long before these antibiotics were introduced.

This paper revealed many fascinating aspects about our ancient microbiomes.  First, it is interesting to see that Firmicutes dominated our ancient flora, especially because Bacteroidetes, which are much more common in our guts today, are broadly associated with health.  Also, it appears that many of the pathogens that afflict all sorts of diseases today have prehistoric counterparts, and may have been more abundant, or even more tolerable long ago.  Finally, the revelation about antibiotic resistance genes show that the mutations that cause them appear common enough that they occurred naturally in thousand year old colons.