Lucky for us, mummification also often preserves the very bacteria that would have consumed a body from within — those microbial guests that live within our guts and play such a major role in preserving our health while we are living. Today, armed with powerful new genetic sequencing tools, scientists are studying the DNA of these mummy microbes for clues about how the gut microbiome, human disease, and antibiotic resistance have evolved.

Egyptian and Chinchorro mummies aren’t great for this kind of research, because both cultures eviscerated their dead before preserving them. But the Incans, who mummified the dead naturally in the high and dry Andean mountains, often left the insides intact. Natural mummification occurs when the water content of a body falls below a critical threshold — from 75–80% down to 20–27% — which dessicates the flesh, arresting bacterial growth. The Medici of Italy also mummified their nobility naturally, first “dripping” fluids from their bodies and then placing them in dry places. Likewise, they left the nobles’ organs untouched.

What they found was remarkable. A high concentration of genes associated with resistance to modern antibiotics — even though these antibiotics were only developed in the last 100 years.

Many Incan mummies were lost when they were moved from their original burial sites by Spanish colonials, but some of them landed in museums in Latin America and Europe. A triplet of mummies from the Andes mountains near Cuzco, Peru, once the seat of the Incan empire, has proven especially revealing to microbiome researchers. One of the three mummies, an Andean woman thought to have lived to around 22 years of age some time between 980 and 1170 AD, was brought to Italy from South America in the second half of the 19th century and now resides at the Museum of Anthropology and Ethnology of the University of Florence, Italy. Microbiologist Raul Cano and colleagues from the U.S., Italy and Puerto Rico, recently decided to take a closer look at her gut bacteria. They extracted DNA from her internal organs, colon, and fossilized paleofeces — basically intact pieces of ancient poop.

What they found was remarkable. A high concentration of genes associated with resistance to modern antibiotics — even though these antibiotics were only developed in the last 100 years. The discovery made sense, since many modern antibiotics are derived from compounds that are naturally produced by soil bacteria. In the arms race of the bacterial world, the ability to defend against the biological weapons of another species instills a competitive advantage, making the species that has it more likely to survive.

In the human world, an examination of the kinds and prevalence of antibiotic resistance genes in these mummified microbes now gives scientists an opportunity to start mapping out how certain antibiotic resistances developed. “Looking at mummies is going to give us a perspective on what’s background noise, and what’s actually caused by the overuse of antibiotics in animal feeds and agriculture,” said Cano. The answers could lead to new drugs to combat today’s antibiotic-resistant microbes and the diseases they cause.

An Andean mummy. Credit: José-Manuel Benito Álvarez)

To get a better read on the background noise, Cano and his colleagues compared antibiotic resistance in different cultures and time periods. All three Andean mummies, including a man and a woman from the 14th–15th century AD, were compared against five mummies of Italian nobility from the Medici period, as well as against modern people living in the Amazon rainforest and modern Italians. The Andean mummy and modern Amazonian guts had much higher proportions of certain antibiotic resistance genes versus the Italian nobility mummy guts: β-lactamases, multidrug transporters, and tetracycline-resistance genes. Cano says that finding seems to support a hypothesis that greater exposure to the natural environment and diets high in soil-contaminated crops could result in a higher proportion of antibiotic-resistance genes, given that the soil is where most antibiotics come from in the first place. Modern Europeans still had the highest proportion of antibiotic resistance genes — likely due to overuse of antibiotics in modern medicine and factory farming.

Cano, who recently left California Polytechnic State University to sign on as chief scientific officer of The BioCollective, a biotech healthcare company, believes the excessive use of antibiotics may be associated with chronic illness in humans, including neurodegenerative diseases. He expects future mummy microbiome research will give us a better picture of what a healthy microbiome looked like prior to the antibiotic era, which may help the company design better probiotics to treat such chronic diseases.

In the meantime, another famous mummy recently provided additional insights into the evolution of modern disease and antibiotic resistance. Otzi the Tyrolean iceman, who died in the Italian Alps and was preserved in mountain ice for over five thousand years, was discovered in 1991. He was thought to have lived in Late Neolithic times, between 3350–3100 B.C. He was very well preserved when found: even his eyeballs and dermis were intact. Among other findings, Italian and Irish researchers identified Heliobacter pylori in Otzi’s gut. H pylori is a human pathogen associated with stomach ulcers and gastric carcinoma, most resembling a strain found in southern and central Asia.

Genetic differences between Otzi’s H. pylori DNA and modern strains suggested to the scientists that todays’ Heliobacter have been subject to “substantial” selective pressure, likely due to modern use of antibiotics. Bacteria evolve under attack, so today’s H. pylori may have adapted to survive a blitz of targeted antibiotics that didn’t exist in Otzi’s time.

Regardless of cures and selective pressures, many modern diseases seem to have been around for a while: the 22-year old Incan mummy showed evidence of Clostridium difficile, which causes an infection of the same name, as well as many types of human papilloma virus, or herpes — suggesting ancient origins and great staying power for these common maladies. Scientists also found evidence that Chagas disease — a tropical parasitic disease caused by the protist Trypanosoma cruzi — may have killed the Incan woman, supporting previous findings that Chagas existed in Latin America before Spanish colonization. Today, Chagas is a major killer in Latin America.

As we continue to study our modern microbiomes and tease out more information from the ancient versions carried by our mummified ancestors, we are bound to find out more about how our complex relationship with our microbes evolved. Perhaps the ancients would have been proud to know that the lore of the mummy’s curse, may in fact, turn out to be a blessing in disguise.