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Fossilized Feces Reveal the Microbiomes of Ancient Japanese Guts

Bacteria in the gut
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The gut contents of ancient Japanese people weren’t too dissimilar from the gut contents of their modern descendants, according to new research.

After analyzing DNA remnants preserved in ancient human coprolites (fossilized feces), the researchers discovered that many of the long-dead bacteria and viruses found in the feces were the same species thriving in present-day Japanese guts.

The research was published in PLOS One.

Gut reactions

The researchers – from Japan’s National Institute of Genetics, the University of Tokyo and the Wakasa History Museum – sampled four coprolites taken from an archeological site in the Fukui Prefecture. The fossilized feces were estimated to have been “left” by people living in the region 7,000-5,500 years ago, during Japan’s Jōmon period.

Despite the degradation of the material, much of the DNA retained in the coprolites was extracted and sequenced at specialized labs at Kitasato University and the University of Tokyo.

After comparing the ancient DNA sequences with a library of modern DNA samples, the researchers found many similarities.

Out of the many viral sequences found in the coprolites, the most abundant originated from the Siphoviridae, Myoviridae, and Podoviridae families – a pattern also observed in the gut viromes of present-day Japanese people.

A similar finding was made regarding the bacterial species; Firmicutes A, Bacteroidota and Verrucomicrobiota bacteria were all highly prevalent in the coprolites, much as they are in many living Japanese guts.

The researchers also came across the DNA of the larger plant and animal species that the ancient Jōmon people would have consumed. These included Vigna angularis (red beans) and Oncorhynchus nerka (salmon) – foods that are still dietary staples in the Fukui region to this day.

“Even though the average length of the reads was too short to analyze genomic variations, we still observed a vast number of reads mapped to the genomes of viruses, bacteria, and likely foods,” the researchers wrote in their conclusion.

“Based on our alignment results, we could estimate the existence of microbes and host– viral coexistence in the Jomon gut environment, comparable to that in present-day humans, suggesting that the coprolites have the potential to reveal long-term host–viral co-evolution trends.”

Under the microbiome

Microbiomes are made up of the bacteria, viruses, and the few fungi species found living in the organs of larger species, including humans. The biomes remain relatively stable throughout an organism’s life, though diet is a key factor in their maintenance. 

The gut microbiome, in particular, is strongly associated with a person’s diet, as its microbes help break down the food that passes through the digestive system.

A study recently published in Nature Microbiology even found that the gut microbiomes of Japanese centenarians were more diverse than other Japanese adults, and included previously unknown bacterial viruses, which may be beneficial to gut health.

Other research has also linked the nature of gut ecosystems to a growing list of conditions, including auto-immune disorders, obesity, and kidney stones.


Reference: Nishimura L, Tanino A, Ajimoto M, et al. Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. PLOS One. 2024. doi: 10.1371/journal.pone.0295924.