A 1,000-Year-Old Mesoamerican Mummy Reveals an Ancient Man’s Microbiome
About 1,000 years ago, Mesoamerican hunter-gatherers wrapped the body of a young man in a bundle, first with a cotton cloth, then with a maguey mat — a thick textile woven from fibers of agave. The body was then placed in a cave in Zimapán, Mexico, where it waited for around a millennium.
But the body, commonly called the Zimapán man, wasn’t alone in its cave. Instead, it was accompanied by the bacteria that inhabited it — the microbiome that survived in the man’s stomach and intestines.
According to a new paper published today in PLOS One, the sequencing of the intestinal tissues and feces of this man has identified the bacteria that populated the bodies of young Mesoamericans around 1,000 years ago, centuries before Spanish colonization.
Read More: Cracking the Cold Case of a 1,000-Year-Old Mummy Murder
Analyzing the Microbiomes of Our Ancient Ancestors
Trillions of bacteria live in our stomachs and intestinal systems, alongside other microorganisms. But the specific bacteria that reside inside our bodies differ from person to person, based on our age, our diet, and our location, among other factors. As such, analyzing the bacteria that took up residence inside our ancient ancestors can provide important insights into their lives.
Previously published studies have sequenced ancient microbiomes, including a microbiome from an Incan individual from the Andes around 1,000 years ago. Aiming to add to this research, Santiago Rosas-Plaza, a genomicist from the National Autonomous University of Mexico, and colleagues studied the mummified body of the Zimapán man, who was probably a forager from the Otopame culture — one of the oldest civilizations in all of Mesoamerica.
Discovered inside a cavern with dry, cool conditions, the body of the Zimapán man was well-preserved with his internal tissues intact, providing a valuable opportunity to assess his microbiome as it was when he died.
Read More: Why Are the World’s Oldest Mummies Deteriorating, And Who Made Them?
Mesoamerican Microorganisms
Using 16S rRNA gene sequencing to test his intestinal tissues and feces, both of which were mummified, the team detected several types of bacteria, including types that are still seen in the human microbiome today.
A) Map of Mexico highlighting in red the state of Hidalgo and the locality of Zimapán, where the individual was recovered. Brown and green shading indicate the regions of Aridoamerica (brown) and Mesoamerica (green). B) Mortuary bundle and remains of the Zimapán individual. C) Samples of paleofeces from the Zimapán individual.
(Image Credit: Rosas-Plaza et al., 2025, PLOS One, CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/))
In fact, bacteria from the Peptostreptococcaceae, Enterobacteriaceae, and Enterococcaceae families were present in the mummy’s intestines and feces, as were bacteria from the Clostridiaceae family, which also appeared in the intestines of the Incan individual, sequenced in the 1990s. Meanwhile, Romboutsia hominis bacteria were found in the Zimapán man’s intestines, too, marking their first appearance in any ancient microbiome.
While some of these bacteria are connected to the digestion of plant tissues, others are tied to the deterioration of insect tissues, suggesting that the man consumed both plants and insects, the former possibly including agaves, yuccas, and the occasional prickly pear.
According to the team, the analysis advances our insights into the Zimapán man, and into ancient microbiomes more broadly. Indeed, little is known about the man, who died in his 20s or 30s, besides what is known about his burial, which suggests that he occupied a prominent position in Otopame society.
“Zimapán man’s remains were neatly wrapped like a bundle, which can be interpreted as indicating that they were an important figure within the community,” Rosas-Plaza and colleagues stated in a press release. “Studying the mathematical composition of the knots within the fabric, we concluded that it was a peculiar and complex arrangement to carry out.”
Additional analysis could spot more surprises in the Zimapán man’s microbiome and could support the findings of the current study. But the results still represent a major step in understanding the lives of ancient Mesoamericans and the ancient bacteria that inhabited them.
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