Desiccated fecal material from the Cave of the Dead Children. (Credit: Johnica Winter, CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/))
DNA from ancient poop shows just how common gut infections really were in early Mexico.
In A Nutshell
- Scientists detected eight different types of gut pathogens in 1,200-year-old dried feces from a Mexican cave, including E. coli, Giardia, pinworms, and Shigella, using targeted DNA testing methods.
- Blastocystis and atypical enteropathogenic E. coli appeared in 70% of samples, while pinworms showed up in 60%, suggesting intestinal infections were common among people living in Mexico’s Rio Zape Valley between 725 and 920 CE.
- This marks the first time researchers have detected several bacterial pathogens in ancient feces using molecular diagnostic techniques, revealing that diseases we consider modern emergencies were routine in the past.
- The findings suggest ancient populations lived with frequent exposure to fecal contamination, facing gut infections without antibiotics, antiparasitic drugs, or clean water systems.
The next time you’re doubled over with food poisoning or your kid brings home pinworms from school, consider this: People in ancient Mexico were dealing with the exact same misery.
Scientists analyzing 1,200-year-old dried feces from a cave in Mexico’s Rio Zape Valley have found the same gut bugs plaguing modern emergency rooms. E. coli O157:H7, the strain that triggers food recalls and hospitalizations today. Giardia, the parasite that ruins camping trips. Pinworms, the bane of elementary schools everywhere. Shigella, which sends travelers running for the bathroom. All of them were there, lurking in the intestines of the Loma San Gabriel people between 725 and 920 CE.
Drew Capone, a researcher at Indiana University’s School of Public Health, led a team that adapted modern hospital diagnostic tools to probe these ancient specimens. The findings, published in PLOS One, uncovered at least one pathogen in every sample tested, with an average of nearly four different bugs per person. The technology mirrors the super-sensitive molecular testing that doctors order when trying to figure out what’s causing a patient’s diarrhea.
Modern Medical Tools Unlock Ancient Health Secrets
Walk into any urgent care clinic today and you’ll hear about the pathogens Capone’s team found. Enterotoxigenic E. coli, detected in half the ancient samples, causes traveler’s diarrhea and kills hundreds of thousands of young children annually in developing countries. Shigella triggers dysentery, with symptoms severe enough that public health departments track it. Giardia remains one of the most common parasitic infections worldwide.
Pinworms topped the prevalence list at 60%, a percentage that would alarm any modern pediatrician. These tiny parasites spread through contaminated surfaces and cause intense anal itching, usually in children. For ancient populations without antiparasitic drugs, chronic infections likely meant chronic discomfort.
Blastocystis, a common intestinal microbe, showed up in 70% of samples. Scientists still debate whether Blastocystis causes symptoms or peacefully coexists in human guts, but its presence in ancient feces mirrors its prevalence in modern populations with poor sanitation.
The Cave of the Dead Children sits in a low-humidity environment that naturally preserved organic material through desiccation. The cave’s contents have been studied for decades using microscopes to identify parasite eggs. But DNA-based methods can detect things microscopes miss, especially bacteria and protozoa that don’t leave behind easily visible eggs.
Capone’s team tested for 30 different enteric pathogens, the same panel that might be ordered for a patient with severe gastrointestinal symptoms. They extracted DNA from ten samples using methods optimized for degraded ancient material, then amplified specific genetic sequences to boost detection.
Bacterial pathogens that had never been detected in ancient feces before appeared in the results. Enterotoxigenic E. coli, enteropathogenic E. coli, Shigella, E. coli O157:H7, and Blastocystis all made their archaeological debut in this study.
Daily Life Meant Constant Contamination
The sheer number and variety of pathogens paint a grim picture. These ancient people were living in an environment contaminated with feces, not occasionally but constantly.
Some pathogens spread through water. Others hitchhike on food. Pinworms spread through hand-to-mouth contact after touching contaminated surfaces. Different transmission routes mean people were getting exposed in multiple ways throughout their daily routines.
Previous dietary studies showed the Loma San Gabriel people ate primarily agave plants, along with maize, beans, cactus, ground cherry, and sunflower. They lived in caves, which provided shelter but also concentrated waste if not managed properly. Without modern sanitation, each meal, each drink of water, each surface touched in communal living spaces represented a potential exposure.
Today, a single case of E. coli O157:H7 triggers public health investigations and food recalls. Finding it in ancient feces means that what we now treat as an emergency outbreak was once just part of life.
Why Different Tests Find Different Things
Earlier research detected strong evidence for Cryptosporidium, a parasite that causes watery diarrhea, in 61% of samples from the same cave using antibody-based tests. Yet the new DNA methods didn’t find Cryptosporidium at all.
Different detection methods find different things. Antibodies and antigens can persist longer than DNA in some cases. Or the DNA might be there but too degraded for modern tests to amplify. Absence of detection doesn’t mean absence of infection.
Similar uncertainty applies to human mitochondrial DNA. Only one sample tested positive for it, despite multiple lines of evidence pointing to human origin for all ten samples. Human mitochondrial DNA naturally occurs at much lower concentrations in feces than bacterial DNA, sometimes by ratios of 9,300 to 1. Over 1,200 years, that initial scarcity may have dropped below detection limits in nine samples.
What Ancient Pathogens Tell Us About Modern Life
Ten samples from one cave can’t tell us about disease across an entire culture. Researchers couldn’t determine how long different genetic material persists in dried feces. DNA damage over time could affect results. Samples weren’t fully homogenized, which may explain why repeat tests sometimes disagreed.
But the core finding remains: The pathogens were there. The same ones making people sick today were making people sick 1,200 years ago.
Modern medicine has changed the equation dramatically. We have clean water, sewage systems, antibiotics, antiparasitic drugs, and public health infrastructure. A child with pinworms gets a single dose of medication and the infection clears. Someone with E. coli poisoning can receive supportive care that prevents death. Giardia is unpleasant but treatable.
The Loma San Gabriel people had none of these advantages. Chronic low-level infections likely sapped energy and stunted growth. Acute outbreaks probably killed vulnerable individuals, especially children and the elderly. The pathogens didn’t need to be exotic or unusual to be deadly. The familiar ones did plenty of damage on their own.
As antibiotic resistance grows and climate change disrupts sanitation systems, some experts worry about returning to conditions where common pathogens pose serious threats again. These ancient fecal samples serve as a reminder of what life looks like without modern interventions. The bugs are timeless. Our defenses against them are not.
Paper Summary
Methodology
Researchers collected ten desiccated fecal samples from the Cave of the Dead Children in Mexico’s Rio Zape Valley. These samples, dated to 725-920 CE, had been stored since a 1993 dietary analysis study. The team extracted DNA using methods optimized for ancient material, which included grinding the fibrous samples, treating with EDTA and Proteinase K, vortexing for 10 minutes, and purifying through specialized columns. They then performed PCR pre-amplification of target sequences to increase the amount of DNA available for testing. Finally, they used custom TaqMan Array Cards to test for 30 different enteric pathogens, parasites, and gut microbes through quantitative PCR. Each sample underwent testing in duplicate or triplicate when sufficient material was available. The team included negative controls throughout the extraction and testing process to monitor for contamination. Additionally, they used digital PCR to test for human mitochondrial DNA to confirm the samples’ human origin.
Results
The research team detected at least one pathogen or gut microbe in all ten samples, with an average of 3.9 targets per sample. Blastocystis appeared in seven samples (70%), atypical enteropathogenic E. coli in seven samples (70%), Enterobius vermicularis (pinworm) in six samples (60%), Entamoeba in five samples (50%), and enterotoxigenic E. coli in five samples (50%). Three samples tested positive for Shigella/enteroinvasive E. coli (30%), two for Giardia (20%), and one for E. coli O157:H7 (10%). All samples tested positive for an enteric bacterial marker (enteric 16S rRNA) designed to detect human fecal material. Only one sample tested positive for human mitochondrial DNA, though at very high concentrations. Among samples tested in multiple replicates, 60% showed perfect agreement (all replicates positive), 5% showed moderate agreement (two of three positive), and 35% showed poor agreement (only one replicate positive).
Limitations
The study analyzed only ten samples from a single cave site, which limits the generalizability of findings. The researchers could not determine how different types of genetic material persist in ancient feces over time, so absence of detection doesn’t necessarily mean a pathogen wasn’t originally present. They did not assess DNA damage through sequencing, which could affect detection rates. PCR inhibitors may have had varying effects on different assays. The samples were not homogenized completely, which may have contributed to variability between replicate tests. The researchers did not work in a dedicated ancient DNA clean room, though they took extensive contamination precautions. Human mitochondrial DNA was detected in only one sample despite other evidence suggesting human origin, possibly due to its naturally lower concentration in feces compared to bacterial markers. The study did not test for animal mitochondrial DNA, so animal contribution to some samples cannot be ruled out. Finally, the researchers could not completely eliminate the possibility of cross-contamination or nonspecific amplification, though no such issues appeared in negative controls.
Funding and Disclosures
Drew Capone received partial support from a National Institute of Environmental Health Sciences T32 Fellowship (5T32ES007018). The authors declared no competing financial interests. The funders had no role in study design, data collection and analysis, the decision to publish, or preparation of the manuscript. No additional external funding was received for this study.
Publication Details
Capone D, Holcomb D, Lai A, Meade T, Reinhard K, Brown J (2025) “Targeted pathogen profiling of ancient feces reveals common enteric infections in the Rio Zape Valley, 725–920 CE,” was published October 22, 2025 in PLOS One 20(10): e0318140. doi:10.1371/journal.pone.0318140
