One day, in a cave north of Durango, Mexico, someone defecated. In fact, there were quite a few of them, and these events were spread over a fairly long period of time – from approximately 725 to 920 AD. researchers now believe. Thanks to the dry conditions of the cave, when archaeologists excavated the site in the 1950s, the excrement was in fairly good shape. Weathered, dry and filled with fiber, these stool samples gave scientists valuable information about what foods ancient people ate and what lived in their guts.
Sediments from the cave are now actively traveling, ending up in various laboratories interested in studying them. In 2021, one global team of employees analyzed the DNA contained in old feces— or paleofec as it's subtly called — to see if they could identify microbes in the gut microbiomes of poop.
Now, in new document published in PLOS OneAnother group of researchers took a new look at DNA taken from 10 feces. Their results largely confirm an earlier discovery: the people who made these poops were host to a menagerie of parasites.
Playing host to worms
Typically, the feces that Drew Capone, the study's lead author, works with are much fresher. An environmental microbiologist at Indiana University, Capone studies how sanitation affects health. “Our work addresses the question: 'How does feces get into the environment?' Where is feces found in the environment? How does the infrastructure prevent feces from entering the environment? And then, how does feces affect children's health?” he says.
Capone and his colleagues were interested in using methods to detect pathogens in modern feces on ancient feces. These methods sort the DNA in a sample looking for specific genes that are signatures of parasites such as pinworms as well as bacterial pathogens.
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To extract this DNA, the researchers had to obtain paleofecal samples from the cave. It turned out to be more difficult than they expected: “We had to grind these ancient feces into powder. We couldn't really break the pieces off,” says Capone. They performed a DNA matching procedure and obtained results indicating that the feces contained a number of different pathogens, including pinworms, the protozoan parasite Giardia, and various pathogenic bacteria.
Many feces were positive for multiple organisms. In Capone's experience, such large numbers of pathogens are not unusual in places with poor sanitation, leading him to suspect that the people who dumped these feces centuries ago were in a similar situation.
Why your choice of technology matters
However, there are reasons why most laboratories working with ancient DNA no longer use these procedures, say Kirsten Bos and Alexander Hubener, ancient DNA specialists at the Max Planck Institute for Evolutionary Anthropology. DNA tends to fall apart over time, becoming worn out and fragmented. Older technique used in PLOS ONE paper prefers longer stretches of DNAwhich means it's hard to be sure that what you're seeing is actually ancient DNA and not modern DNA that got there by accident. Laboratories specializing in the study of ancient DNA have high-tech clean rooms to minimize contamination. They also use next-generation sequencing optimized for such a fragile substance.
In addition, most laboratories test the ends of DNA fragments where characteristic abrasions are observed to confirm that what they are looking at is indeed old. Using technology in PLOS ONE In the paper, “you can't easily tell whether these chemical modifications that occur in ancient DNA occurred,” Bos says.
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Capone argues that many of the organisms tested are not able to survive for long outside the human intestine, so the risk of getting a false positive from modern DNA collected during travel in feces may be quite small. Additionally, specialized laboratory testing of ancient DNA can be expensive, while this older method is more affordable.
Hubener, who was part of the team working on the 2021 study of fecal samples from the cave, says he is skeptical about matches with bacteria—they can be especially difficult to identify in ancient samples using this method. However, given what his team found and what we know about parasite biology, he says the results from studies of larger parasites such as worms are on somewhat more solid ground. “To me it’s plausible,” Hubener says.
“What would be particularly interesting is to use both old and new methods on the same samples,” says Bos. This would make it clear what the old methods can reliably detect that the newer, more rigorous procedures also find.
“That would be a really good way to move things forward,” she says.
