1,000-year-old gut microbiome revealed for young man who lived in pre-Hispanic Mexico

(Press-News.org) Analysis of preserved feces and intestinal tissue has revealed specific types of bacteria that were present in the microbiome of a young adult man who lived in Mexico about 1,000 years ago, prior to Spanish colonization. Santiago Rosas-Plaza of Universidad Nacional Autónoma de México and colleagues present these findings in the open-access journal PLOS One on October 8, 2025.

The human gut microbiome consists of microorganisms, including bacteria, that naturally live in people’s intestines. Certain types of bacteria are widely associated with the human gut microbiome, but a person’s particular mix of bacteria may vary depending on factors such as age, diet, health, and where they live. Studying ancient microbiomes using mummies and human remains can therefore deepen understanding of ancient populations and show how the human microbiome may have changed over time.

A growing number of ancient microbiomes have been revealed, including for an ancient Incan person and Germany’s “Tyrolean Iceman.” To further expand the field, Rosas-Plaza and colleagues analyzed the exceptionally well-preserved remains of a man discovered in a rock shelter in Zimapán, Mexico. Prior analyses suggest the “Zimapán man” was most likely a seasonal seminomadic hunter-gatherer who was part of the ancient Mesoamerican Otopame culture and died about 1,000 years ago between the ages of 21 and 35.

To determine which types of bacteria may have been present in the man’s microbiome, the researchers applied a standard method known as 16S rRNA gene sequencing to his mummified intestinal tissue and preserved feces.

They found several families of bacteria associated with the human microbiome, including Peptostreptococcaceae, Enterobacteriaceae, and Enterococcaceae. They also detected high levels of bacteria in the Clostridiaceae family, which have previously been found in intestinal tissue of mummies from ancient Andean civilizations. The remains also contained some bacteria, such as Romboutsia hominis, that are associated with the modern human gut microbiome, but have not been found in ancient microbiomes until now.

These findings expand knowledge of ancient microbiomes and could provide clues to the Zimapán man’s life. Further analysis will be needed confirm these results and determine the complete composition of the Zimapán man’s microbiome.

The authors add: “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. The outer layer of the bundle was made of a mat, that is, long fibers, apparently maguey, intertwined to form a strong yet malleable rectangle. Beneath this mat, and on top of which Zimapán man was placed, was a perfectly woven sheet of native brown cotton. Studying the mathematical composition of the knots within the fabric, we concluded that it was a peculiar and complex arrangement to carry out. For almost eight years now, Master Luisa Mainauo, who safeguards the mortuary bundle, has been working with her team to restore the savannah and soon be able to show it not only to the people of Mexico but to the entire world.”

 

 

In your coverage, please use this URL to provide access to the freely available article in PLOS One: http://plos.io/46iRuEK

Citation: Rosas-Plaza S, Mainou L, Delgado G, Morales R, Aguilar-Romero A, Escalante AE, et al. (2025) Microbiome characterization of a pre-Hispanic man from Zimapán, Mexico: Insights into ancient gut microbial communities. PLoS One 20(10): e0331137. https://doi.org/10.1371/journal.pone.0331137

Author countries: Mexico

Funding: The author(s) received no specific funding for this work.

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