It’s a really big deal when fossilized feces survive the ravages of time. These hardened pieces of excrement open up a window into what animals ate thousands of years ago and even what may have made them sick. Humans are not exempt from this, with dried human feces indicating we have always loved cheese and beer and that our microbiome has evolved over thousands of years.
DNA recovered from 1,000-year-old dried feces indicates that intestinal infections from pinworm or Shingella may have plagued ancient people living in present day northern Mexico’s Rio Zape Valley. The DNA and what it tells us is detailed in a study published today in the journal PLOS One.
For scientists digging into the past, ancient feces are a time capsule of intestinal parasites, food, and more. While microbial DNA can survive in stool samples, the analysis can be difficult since DNA degrades over time.
“Measuring pathogens in ancient fecal samples is an absolutely fascinating challenge,” study co-author and University of North Carolina at Chapel Hill environmental engineer Joe Brown tells Popular Science. “It can inform our understanding of the health of people living in a very different time and place. We really sought to bring new and highly specific methods–previously only used on modern samples–to analysis of samples from the Rio Zape site.”
In the study, they looked at fecal samples uncovered from La Cueva de Los Muertos Chiquitos, or the “Cave of the Dead Children,” in the state of Durango, Mexico. It was populated by the Loma San Gabriel people about 1,200 to 1,400 years ago. The fecal samples themselves are about 1,100 to 1,300 years old.
The region’s low humidity and dry climate helped preserve the fecal samples and other finds that have been recovered from the cave since it was first excavated in the middle of the 20th century.
“The Cave of the Dead Children, gets its name because more than a dozen skeletons from children were found during the excavation,” study co-author and Indiana University environmental health microbiologist Drew Capone tells Popular Science. “More than 500 ancient desiccated fecal samples and over 2,000 kids were also recovered from the cave.”
The team used a new technique to analyze 10 samples. Previously, most work with ancient fecal material like this has used DNA sequencing. While useful, DNA sequencing is more untargeted. It will give a sequence for all of the DNA that is present in the sample, but can miss the less concentrated microbes frequently found in ancient feces.
“We used validated qPCR assays to look for genes that are specific to enteric pathogens,” says Capone. “This qPCR based approach has a lower limit of detection than sequencing.
With this different technique, the team identified the genetic signatures of a wide array of gut parasites, including the protozoan Blastocystis and multiple strains of bacterial E. coli. These pathogens have never been detected in ancient feces. Additionally some pathogens, including pinworm, were present in the majority of samples.
For Capone, this high precedence of pinworm was incredibly surprising, given that the samples were over 1,000 years old and the DNA would have been highly degraded over such a long period of time.
“When working with modern samples we are incredibly careful about storing our samples in ultra-low temperature freezers to minimize degradation before analysis,” he says. “I was incredibly surprised that even after 1,000+ years DNA from these pathogens had persisted at detectable levels.”
According to the team, this kind of work offers a proof-of-concept for using qPCR to identify intestinal parasites of past human populations. Some of these pathogens are human-specific, including pinworm and Shigella, which indicates that this is a way to distinguish human infected from the waste of other species.
This high prevalence of gut parasites potentially indicates that intestinal infections and poor sanitation were common among the Loma San Gabriel. However, since the study was only limited to 10 samples and targeted a list of well-studied pathogens, it is difficult to say. Future studies using larger samples could give a more complete assessment of the pathogens that plagued our ancestors.
“There is a lot of potential in the application of modern molecular methods to inform studies of the past,” Brown added in an accompanying statement. “Highly sensitive and specific targeted assays can complement sequencing approaches when specific targets are of interest. We look forward to continuing this collaborative work to better understand the presence and movement of pathogens in ancient samples.”
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