The Forgotten Gut of Zimapán

When archaeologists unwrapped the funerary bundle from the rock shelter near Zimapán, Mexico, they found a young man preserved by time and desert air. His body was wrapped carefully in woven maguey fibers and cotton, folded in layers that suggested reverence, not haste. For nearly a millennium, the silence of the Sierra Madre had kept him intact—skin, tissue, and even traces of his inner world.

The Zimapán man, also referred to as Hna Hnu, was a resident of the Mesoamerican border who lived 1,000 years ago. The image shows the moment when Hna Hnu’s body was opened. This body was found inside a cave in a dry environment, which allowed their remains to remain for nearly 1,000 years. From the remains, we were able to isolate a coprolite and intestinal tissue, which was used to extract the DNA of the bacteria still present at the time of Hna Hnu’s life. From this genetic material, we were able to recover their gut microbiome community. Bacteria associated with the degradation of complex plant tissue and even, very likely, with the degradation of insect molecules such as those of the Clostridium genus were discovered. Hna Hnu provided us with valuable information about the association between the microbiome and diet. Credit: Rene Cerritos Flores, CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

Now, thanks to advances in microbial genomics¹, that inner world is speaking again. Within his desiccated intestines and preserved feces, scientists have recovered one of the oldest gut microbiomes ever sequenced in the Americas. What they found is more than a catalogue of bacteria—it is a glimpse into how pre-Hispanic people lived, ate, and interacted with their environment before colonial disruption transformed both bodies and ecosystems.

“The microbiome is like a molecular diary,” says Dr. Elena Rossi, a bioarchaeologist at the University of Bologna. “It records the foods consumed, the pathogens encountered, and even the ecological rhythms a person’s body once mirrored.”