Examination of 14th and 15th century latrines in Jerusalem and Riga, Latvia, identifies some of the microbes that colonized the gut of these pre-industrial populations and sheds light on how the human gut microbiome has changed since the Middle Ages.
Innovative methods for the reconstruction and determination of the DNA of ancient bacteria from archaeological finds have been groundbreaking in recent years in researching past epidemics. A new study now reports on the first attempt to use these methods to determine the microbial diversity of the medieval intestinal microbiome. The results of the study provide insights into the microbiomes of pre-industrial agricultural populations and could provide the much-needed background for understanding the health of modern microbiomes.
Over the years, research has found that the microbiomes of people in industrialized societies are significantly different from the microbiomes of people living in hunter-gatherer communities. A growing body of knowledge also points to a connection between changes in the microbiome and many diseases in the industrialized world, such as inflammatory bowel disease, allergies and obesity. The current study helps to describe the changes in gut microbiomes and underlines the importance of archaeological latrines as a source of bio-molecular information.
Centuries-old feces as a source of molecular information?
Piers Mitchell of Cambridge University specializes in the good contents of past people through analysis of unusual substrates. By looking at the contents of archaeological latrines and desiccated faeces under the microscope, he and his team have learned volumes about the intestinal parasites that plagued our ancestors.
Piers Mitchell of Cambridge University specializes in studying the intestinal contents of individuals from the past. By looking at sediments from archaeological latrines and dried-up feces under a microscope, he and his team have gained extensive knowledge of the intestinal parasites that plagued our ancestors.
"Microscopic analysis can show the eggs of parasitic worms that lived in the gut, but many microbes in the gut are just too small to see," explains Mitchell. "If we want to find out what makes a healthy microbiome for modern humans, we should look at the microbiomes of our ancestors, who lived before the use of antibiotics, fast food and other traps of industrialization."
Kirsten Bos, specialist in ancient bacterial DNA from the Max Planck Institute for the History of Human History and co-director of the study, was initially skeptical as to whether it was feasible to analyze the contents of the medieval latrines.
"In the beginning we weren't sure whether molecular signatures of intestinal contents in the latrines could have survived for hundreds of years, and whether we would be able to distinguish them from a presumably dominant environmental signal. So far we have been able to find old bacterial DNA mainly from calcified tissue such as bone or extract tartar, which offer completely different preservation conditions, "explains Bos." Nevertheless, "she continues," I naturally hoped that our data would change my point of view."
The team analyzed sediments from medieval latrines in Jerusalem and Riga, Latvia, from the 14th and 15th centuries. The first challenge was to distinguish the bacteria that once belonged to a human microbiome from the bacteria that got into the latrines through the environment.
The research team identified a wide range of bacteria, archaea, protozoa, parasitic worms, fungi, and other organisms, including many species known to be found in the intestines of modern humans.
"It appears that latrines are indeed valuable sources of both microscopic and molecular information," concludes Bos.
Old and modern microbiomes are fundamentally different
Susanna Sabin, a former doctoral student at the Max Planck Institute for the History of Human History and first author of the study, compared the DNA from the latrines with the DNA from other sources, including microbiomes from populations from industrialized countries and hunter-gatherer communities, as well as from sewage and soil.
"We found that the microbiomes in Jerusalem and Riga shared some common characteristics. And they are similar to modern hunter-gatherer microbiomes and microbiomes from people from industrialized countries. Yet they were so different that they formed a separate group. We do not know of any modern source containing the same microbial content as what we found in the medieval latrines ".
Studying latrines where many people's feces mingled gave the research team an unprecedented look into the microbiomes of entire communities.
"These latrines gave us much more representative information about the broader pre-industrial populations of these regions than we could have obtained from a single droppings sample," explains Mitchell. "The combination of evidence from light microscopy and analysis of ancient DNA allows us to identify the amazing variety of organisms that lived in the gut of our ancestors."
Although the new approach to studying the microbiome looks extremely promising, challenges remain.
"We'll need a lot more studies at other archaeological sites and at other time periods to fully understand how the microbiome of human populations has changed over time," says Bos. "Nevertheless, we have taken a decisive step by showing that the extraction of DNA from archaeological latrines can work."
Sabin S, Yeh H-Y, Pluskowski A, Clamer C, Mitchell PD, Bos KI. Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities. Philosophical Transactions of the Royal Society B: Biological Sciences. 2020;375(1812):20190576. doi:10.1098/rstb.2019.0576
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