Traces of Gut Microbiomes Discovered in Medieval Toilets

Through ancient cesspits, archaeologists are able to get a glimpse on ancient humans’ diet, health, and habits. Just recently, archaeologists conducted an analysis of two cesspits — or latrines — in Latvia and Israel to study the historical people’s intestinal microbiomes, which could be different from the microbiomes of both modern people and prehistoric hunter-gatherers.

Gut microbiomes encompass all the microbes found in the intestines, including bacteria, viruses, and fungi. By studying microbial communities in medieval times, scientists can study ancient diet and digestion as well as track the changes that occurred to the people’s diets over time, giving us a clear idea of the health of modern microbiomes.

The researchers examined a 14th-century cesspit in Riga and a 15th-century cesspit in Jerusalem. During the time when the cesspits were being used, the areas were urban but not necessarily industrialised, which meant the users of the latrines probably ate food different from modern city dwellers. The sites were also chosen because the two different geographic regions could mean the populations had different microbiomes.

According to Piers Mitchell, a co-author of the study, the medieval period was sufficiently old for them to detect change compared with modern populations. Furthermore, the period was not too old that the DNA would not survive.

The investigation confirmed the scientists’ suspicions, revealing that the remnants of Treponema bacteria were found in the guts of modern hunter-gatherers but not in those of industrialised people. They also found Bifidobacterium in the guts of industrialised people but not in the hunter-gatherers. The researchers describe these differences as the result of a dietary trade-off.

Co-lead author Sussana Sabin, an archaeologist at the Max Planck Institute for the Science of Human History in Germany, believes there is no known modern source that harbours the microbial content seen in the study.

In addition, the presence of both types of gut bacteria could either reflect diversity among the residents of the city or indicate that medieval humans had microbiomes different from what modern humans have today.

Co-lead author Kirsten Bos from the Max Planck Institute says that they were not even certain if the molecular signatures of gut contents would even survive in the latrines after hundreds of years. The conditions of their bacteria would be different from other successful ancient bacterial retrieval, which came from calcified tissues and dental calculus and were preserved differently.

Researchers first had to distinguish the gut microbes from those normally occurring in the surrounding soil. They then found evidence of a range of bacteria, archaea, protozoa, parasitic worms, and fungi.

This was not the first time cesspits were used by archaeologists to look for information. During previous studies conducted on old latrines, researchers were able to find remains like parasite eggs, which could be examined with a microscope.

However, the traditional techniques would not be able to look at the organisms examined in the new research, which were much too small. Instead, the researchers used metagenomics or the study of microorganisms through DNA extraction. The researchers hope their techniques will help other researchers analyse gut biomes from ancient times and places to give us a clearer glimpse of historical diet changes.

Mitchell believes that in order to determine what constitutes a healthy microbiome for modern people, we need to start looking at ancient microbiomes of people who lived before the dawn of antibiotics, fast food, and other modern trappings.

Traces of Gut Microbiomes Discovered in Medieval Toilets

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