Scientists have reported what they say is the first attempt to use the methods of ancient bacterial detection, pioneered in studies of past epidemics, to characterise the microbial diversity of ancient gut contents from two medieval latrines.
The findings, published in Philosophical Transactions of the Royal Society B, provide insights into the microbiomes of pre-industrial agricultural populations.
And those insights are worth having, they say, because they may provide much-needed context for interpreting the health of modern microbiomes.
“If we are to determine what constitutes a healthy microbiome for modern people, we should start looking at the microbiomes of our ancestors who lived before antibiotic use, fast food, and the other trappings of industrialisation,” says Piers Mitchell from Cambridge University, UK.
Co-lead author Kirsten Bos, a specialist in ancient bacterial DNA from Germany’s Max Planck Institute for the Science of Human History, admits she was initially sceptical about the feasibility of investigating the contents of latrines that had long been out of order.
“At the outset we weren’t sure if molecular signatures of gut contents would survive in the latrines over hundreds of years,” she says. “Many of our successes in ancient bacterial retrieval thus far have come from calcified tissues like bones and dental calculus, which offer very different preservation conditions.”
With an open mind, the team analysed sediment from latrines in Jerusalem and Riga, Latvia, dating from the 14th-15th century CE.
The first challenge was distinguishing bacteria that once formed the ancient gut from those normally found in the soil – an unavoidable consequence of working with archaeological material.
Once that was overcome, the researchers found that latrines, where the faeces of many people are mixed together, provided insight into the microbiomes of entire communities.
They identified a wide range of bacteria, archaea, protozoa, parasitic worms, fungi and other organisms, including many taxa known to inhabit the intestines of modern humans.
They then compared the latrine DNA to those from other sources, including microbiomes from industrial and foraging populations, as well as wastewater and soil.
“We found that the microbiome at Jerusalem and Riga had some common characteristics: they did show similarity to modern hunter gatherer microbiomes and modern industrial microbiomes, but were different enough that they formed their own unique group,” says Bos’s colleague and a co-lead author, Susanna Sabin.
“We don’t know of a modern source that harbours the microbial content we see here.”
Despite the promise of this new approach for investigating the microbiome, challenges remain.
“We’ll need many more studies at other archaeological sites and time periods to fully understand how the microbiome changed in human groups over time,” says Bos. “However, we have taken a key step in showing that DNA recovery of ancient intestinal contents from past latrines can work.”