Study seeks to compare microbiomes of our ancestors for clues to modern diseases

Over the years, scientists have noted that those living in industrialized societies have a notably different microbiome compared to hunter-gatherer communities around the world. From this, a growing body of evidence has linked changes in our microbiome to many of the diseases of the modern industrialized world, such as inflammatory bowel disease, allergies, and obesity.

A new study published this week demonstrates a first attempt at using the methods of ancient bacterial detection to characterize the microbial diversity of ancient intestinal contents from two medieval latrines. The findings provide insights into the microbiomes of pre-industrial agricultural population, which may provide much-needed context for interpreting the health of modern microbiomes.

Analysis of 14th-15th century latrines in Jerusalem and Riga, Latvia identifies some of the microbes resident in the intestines of these pre-industrial population, revealing how gut contents have changed since medieval times. This could help scientists understand if changes to our microbiome – the genetic makeup of the bacteria, virus, fungi, parasites, and other microbes living inside us – affect modern-day afflictions.

The first challenge was distinguishing bacteria that once formed the ancient gut from those that were introduced by the environment. The researchers identified a wide range of bacteria, parasitic worms, archaea, protozoa, fungi, and other organisms known to inhabit the intestines of modern humans.

“It seems latrines are indeed valuable sources for both microscopic and molecular information,” said Kirsten Bos, a specialist in ancient bacterial DNA from the Max Planck Institute for the Science of Human History.

Piers Mitchell, a Cambridge University paleopathologist, said ancient latrines could become a key source of biomolecular information and allow scientists to explain how modern lifestyles affect human health.

“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,” he said.

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What researchers found?

Researchers compared the DNA samples from the latrine to those from other sources, including microbiomes from industrial and foraging populations, as well as waste water and soil. They found that the microbiome at Jerusalem and Riga did show similarity to modern hunter-gatherer and modern industrial microbiomes, but were different enough that they formed their own unique group.

The researchers got an extraordinary insight into the microbiomes of entire communities since the latrines contain mixed faeces of many people.

“These latrines gave us much more representative information about the wider pre-industrial population of these regions than an individual faecal sample would have,” explains Mitchell. “Combining evidence from light microscopy and ancient DNA analysis allows us to identify the amazing variety of organisms present in the intestines of our ancestors who lived centuries ago.”

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