Deep within a cave in Zimapán, Mexico, a remarkable discovery has opened a new window into the microbial world of ancient human guts. Archaeologists and microbiologists collaborating from Universidad Nacional Autónoma de México have successfully characterized the gut microbiome of a pre-Hispanic man who lived nearly a millennium ago. This extraordinary achievement offers an unprecedented glimpse into the microbial ecosystem inhabiting ancient human intestines, shedding new light on the interactions between diet, environment, and gut bacteria before the radical shifts introduced by European colonization.
The remains, found in a dry cave shelter within the Mesoamerican border region, preserved the body of a young adult man, believed to have been a seasonal seminomadic hunter-gatherer belonging to the Otopame culture. Radiocarbon dating estimates this individual died roughly 1,000 years ago, providing an invaluable snapshot of microbial life in the pre-Hispanic period. The exceptional preservation of his remains, a result of the arid environment, allowed scientists not only to extract DNA from intestinal tissues but also to analyze coprolites—fossilized feces—providing complementary viewpoints on bacterial populations.
Using state-of-the-art molecular techniques centered around 16S ribosomal RNA gene sequencing, researchers identified a diverse array of bacterial taxa inhabiting the ancient gut milieu. This method targets a highly conserved genetic marker ubiquitous among bacteria, enabling precise discrimination between different microbial species even in degraded ancient samples. The study reported the presence of bacterial families long linked with human intestinal health, including Peptostreptococcaceae, Enterobacteriaceae, and Enterococcaceae, confirming that core microbial groups have persisted through centuries.
Intriguingly, the team discovered elevated levels of Clostridiaceae, a family of bacteria previously documented in mummified tissue from Andean civilizations, known for their role in fermenting complex molecules and producing short-chain fatty acids vital for intestinal health. The prominence of these bacteria suggests that similar anaerobic fermentative processes were integral to the pre-Hispanic human gut, influencing digestion and immune responses. Moreover, the detection of Romboutsia hominis, a bacterium common in modern gut microbiomes but not previously found in ancient samples, points to evolutionary continuities and possibly adaptive functions conserved across time.
Beyond taxonomic identification, the findings intimate dietary habits and ecological interactions shaping the microbiome. The presence of bacteria specializing in the degradation of complex plant fibers underscores a diet rich in plant-based components. Furthermore, some detected bacteria belong to genera capable of metabolizing insect molecules, reflecting entomophagy—the consumption of insects—as a plausible nutritional source for this ancient population. These microbial signatures enable reconstructions of lifestyle and subsistence strategies practiced a millennium ago in Mesoamerica.
The intricacy of microbiome composition offers a window into human adaptation and health before the drastic lifestyle changes brought by European conquest. By comparing ancient and modern gut microbial communities, scientists hope to unravel how factors like diet modernization, antibiotic use, and urbanization have reshaped the human microbiota. Such insights hold promise for understanding contemporary diseases linked to microbiome disruption, such as metabolic syndromes and autoimmune conditions.
The individual’s mortuary context also offers cultural insights. The “Zimapán man” was meticulously wrapped in a multi-layered burial bundle, with an outer mat woven from maguey fibers and an inner sheet of intricately knotted native brown cotton. This elaborate preparation suggests high social status or ritual significance, hinting at complex cultural practices surrounding death and remembrance among the Otopame. The detailed craftsmanship of the textiles complements the biological narrative, revealing layers of human ingenuity intertwined with microbial ecology.
These preliminary results mark a significant step in ancient microbiome research but also underscore the need for comprehensive analyses to reconstruct the full microbial community and its functional potential. The researchers acknowledge the limitations inherent in ancient DNA studies, including contamination risks and DNA degradation over time. Future work deploying shotgun metagenomics and proteomics could provide deeper resolution of microbial genomes, metabolic pathways, and host-microbe interactions in ancient individuals.
By connecting microbiology, archaeology, and anthropology, this interdisciplinary effort enhances our understanding of human history, health evolution, and microbial biodiversity. The Zimapán man’s gut microbiome serves as a microbial time capsule, illuminating the symbiotic relationships foundational to human biology long before industrialization. As research progresses, such ancient microbiomes may unravel how human-microbial partnerships have co-evolved and adapted through environmental challenges and cultural transformations.
This landmark study was published open-access in PLOS One on October 8, 2025, authored by Rosas-Plaza et al., and represents a pioneering contribution to paleo-microbiology. The work exemplifies the power of modern molecular tools to recover the invisible yet essential microbial companions that have journeyed with humanity across centuries. Through these scientific advancements, the ancient microbial inhabitants of our ancestors’ guts are finally coming into light, promising revelations about our evolutionary past and future health trajectories.
The preservation and restoration initiatives for this mortuary bundle, led by Master Luisa Mainauo and her team, aim to safeguard this cultural and biological heritage. Once fully conserved, the site and its findings will be accessible to both Mexicans and the international community, fostering appreciation for the deep connections binding humans, their microbes, and their cultural legacy. This blend of scientific discovery and heritage conservation emphasizes the importance of multidisciplinary approaches in unraveling the complex histories encoded within archaeological remains.
In summation, the microbiome analysis of the Zimapán man offers a compelling narrative bridging ancient lifestyles, microbial ecosystems, and health. It invites further exploration into the enduring relationships between people and their microscopic allies, offering a holistic perspective on human evolution grounded in the intimate and microscopic scale of gut communities. This study sets a precedent for ancient microbiome research, promising to reshape our understanding of the interplay between microbes and human history.
Subject of Research: People
Article Title: Microbiome characterization of a pre-Hispanic man from Zimapán, Mexico: Insights into ancient gut microbial communities
News Publication Date: 8-Oct-2025
Web References: http://dx.doi.org/10.1371/journal.pone.0331137
References: 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.
Image Credits: Rene Cerritos Flores, CC-BY 4.0
Keywords: ancient microbiome, pre-Hispanic Mexico, Zimapán man, gut bacteria, 16S rRNA sequencing, paleo-microbiology, mummified intestines, coprolite analysis, Clostridiaceae, Romboutsia hominis, ancient diet, microbial evolution
