About 1,000 years ago, Mesoamerican hunter-gatherers wrapped a young man’s body in a bundle, first with a cotton cloth, then with a maguey mat – a thick textile woven from agave fibers. The body was then placed in a cave in Zimapán, Mexico, where it waited for approximately a millennium.
But the body, commonly known as the Zimapán Man, was not alone in his cave. Instead, it was accompanied by the bacteria that inhabited it – the microbiome that survived in the human stomach and intestines.
According to a new article published today in PLOS OneSequencing this man’s intestinal tissue and stool helped identify the bacteria that populated the bodies of young Mesoamericans around 1,000 years ago, centuries before Spanish colonization.
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Analyzing the microbiomes of our ancient ancestors
Billions of bacteria live in our stomach and intestinal system, alongside other microorganisms. But the specific bacteria that reside inside our bodies differ from person to person, depending on our age, diet, and location, among other factors. So, analyzing the bacteria that called our ancient ancestors home can provide important insights into their lives.
Previously published studies have sequenced ancient microbiomes, including that of an Inca individual from the Andes around 1,000 years ago. To complement this research, Santiago Rosas-Plaza, a genomicist from the National Autonomous University of Mexico, and his colleagues studied the mummified body of Zimapán Man, who was likely a forager from the Otopame culture, one of the oldest civilizations in all of Mesoamerica.
Discovered in a cave with dry and cool conditions, the Zimapán Man’s body was well preserved with its internal tissues intact, providing a valuable opportunity to assess its microbiome as it was at the time of its death.
Learn more: Why are the world’s oldest mummies deteriorating and who made them?
Mesoamerican microorganisms
Using 16S rRNA gene sequencing to test its intestinal tissue and stool, both mummified, the team detected several types of bacteria, including types still present 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 found. Brown and green shades indicate the regions of Aridoamerica (brown) and Mesoamerica (green). B) Mortuary package and remains of the individual Zimapán. C) Paleofeces samples 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 Peptostreptococcaceae, EnterobacteriaAnd Enterococcaceae families were present in the intestines and stools of the mummy, as were the bacteria from the Clostridiaceae family, also appeared in the intestines of the Inca individual, sequenced in the 1990s. In the meantime, The Romboutsia man bacteria were also found in the intestines of the Zimapán man, marking their first appearance in an ancient microbiome.
While some of these bacteria are linked to the digestion of plant tissues, others are linked to the deterioration of insect tissues, suggesting that humans consumed both plants and insects, the former of which may have included agaves, yuccas, and occasionally prickly pears.
According to the team, the analysis advances our knowledge of Zimapán man and more broadly of ancient microbiomes. Indeed, little is known about the man, who died between the ages of 20 and 30, apart from what is known about his burial, which suggests that he occupied an important position in Otopame society.
“The remains of the Zimapán man were carefully wrapped like a package, which can be interpreted to indicate that he was an important figure within the community,” Rosas-Plaza and colleagues said in a press release. “By studying the mathematical composition of the knots in the fabric, we concluded that this was a particular and complex arrangement to achieve.”
Additional analysis could spot other surprises in the Zimapán man’s microbiome and could support the current study’s findings. 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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