Ancient latrines contain DNA clues about past diets, hunting, and animal domestication

Using new DNA analysis methods, researchers examined parasite eggs from ancient latrine sites in Europe and the Middle East.

As every TV detective rifling through a suspect’s trashcan will tell you, you can learn a lot about a person from their waste. Now, with the help of improving DNA analysis techniques, researchers are seeing what they can learn from particularly old waste: that found in ancient latrines. Their study used DNA analysis to identify parasite eggs from latrines at archaeological sites in Bahrain, Jordan, Denmark, the Netherlands, and Lithuania. The oldest sample, from Bahrain, was from 500 BC. The newest was from a Dutch latrine that would have been used around 1700 AD. By identifying parasites associated with different animals, the research offers a glimpse into what people in these particular places and times ate, as well as which animals they shared their living spaces with.

We spoke with study author Martin S?e to learn more about his findings and the techniques that made them possible.

Ancient latrines in Odense. CC-BY S?e et al (2018)

ResearchGate: Can you tell us a bit about the latrines in the study?

Martin S?e: The latrines and deposit samples were chosen because they contain human-specific parasite remains, namely eggs from the human roundworm and whipworm. This shows that human feces were present in the samples. Latrine samples were collected as broadly as our network—and extensive email correspondence—allowed. We found it important to analyze as many samples as possible, from as many different locations as possible, in order to paint a picture of how the interplay between parasite, animal, and plant DNA remains can tell a story.

The samples themselves looked mostly like soil with high organic content. Some, the most recent ones, still smelled or had a brown color and texture that made it very clear what was in front of you. For the older samples and those from the Middle East, it was much less obvious.

RG: Why is the DNA from these latrines still around to be analyzed?

S?e: It is well known that DNA survives for thousands of years, despite all the surrounding tissue and any recognizable structures having broken down. It is still unclear how DNA can remain for thousands of years in dirt and soil samples. In this study, the focus was on the parasites, from which eggs were identified and DNA sequenced.

RG: How did you analyze these samples?

S?e: We extracted the parasite eggs through well-established filtering and flotation methods. I’ve often heard that this requires large sample sizes, which is not compatible with an archaeological sample. We found this to be untrue, as many archaeologists were very willing to help out, sharing as many samples, and as big a sample size, as they could spare.

After filtering and flotation, the samples were split. One part was submitted to standard microscopic evaluation to identify human parasite eggs, and nine parts were submitted to DNA extraction and sequencing, using state-of-the-art ancient DNA laboratories and methods. Finally, bioinformatics helped identify DNA sequences with unique identifiers of mitochondrial genomic DNA regions from specific organisms. This final process proved more difficult than anticipated, as most of the DNA sequences were filtered away—either because they were not mapping to the mitochondria or because they could stem from more than one specific organism. In the end more than 1,000,000,000 DNA reads were generated and only around 600,000 were used for analysis.

RG: What did you find?

S?e: It is clear that humans across the globe are infected with roundworm and whipworm, and have been for thousands of years. More interesting, perhaps, was finding lesser-known parasites, such as tapeworms. We found DNA from fish tapeworm in Viborg, a Viking-age settlement that must have sustained itself through hunting and fishing. DNA from animals found in the same location show the presence of fin whale and roe deer, linking perfectly with a fishing- and hunting-based way of life.

Later samples from Copenhagen and Odense, Denmark show the presence of pig tapeworm, indicating that pigs were used as livestock. We also found a number of instances of Trichuris muris, a rodent whipworm, in a latrine in Odense and in environmental samples from Copenhangen’s Gammel Strand. This shows that mice or rats frequented these places. Samples from Gammel Strand are especially interesting, as they form part of the old harbor of Copenhagen. We also identified DNA from herring and cod there, as well as cats, horses and rats. It was likely a very dirty place by our standards, with a lot of activity from humans and animals.

RG: What else does that DNA information tell us about how the people using the latrines lived?

S?e: Perhaps most straightforwardly, people used latrines for much more than their own feces. The presence of parasite eggs from pig tapeworm, horse roundworm, mouse whipworm, and sheep and goat tapeworm clearly shows that feces from these animals were also thrown into the latrines. This indicates that the animals lived in the close proximity to the sampled locations. The identification of fish and pig tapeworms shows that people ate raw or undercooked meat.

Less surprisingly, people lived together with a lot of unwanted parasites. Human roundworm and whipworm are still the most prevalent worldwide today, though only in the developing world. Enterobius and pinworm are perhaps the only ones still regularly found in Northern Europe.

RG: How does this study fit into the broader research landscape?

S?e: Our findings are basically two-fold. First, that the remains of parasite, animal, and plant DNA can paint a picture of how humans lived in a given place and time. Second, by using shotgun sequencing, we obtained a broad sampling of the DNA remaining in the samples. This DNA was then pieced together into complete mitochondrial genomes for human roundworm, human whipworm, and mouse whipworm.

In the future, studies will generate complete nuclear genomes of various ancient parasites using shotgun sequencing approaches. Such information can be very useful in understanding how parasites have spread across the globe, and how they have adapted to different environments on their way.

One big question is how human parasites, especially human whipworm, spread across the globe. Before it can infect another human host, human whipworm requires a given amount of heat for a specific time in the outside environment, which is not compatible with transmission from human to human in near Arctic climates at the Bering Strait. So did human parasites in the New World adapt to the cold of the Arctic during their dispersal into the Americas, or did they get there by other means? More research in this area may help answer those questions.