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Modern humans may be losing microbial diversity, show teeth samples from Bronze Age

Higher diversity of bacteria involved in gum disease found in 4,000-year-old teeth from a limestone cave


Ancient human teeth could also provide information on how the oral microbiome has evolved over the years. Photo for representation: iStock

Researchers looking at teeth samples from the Bronze Age have found the bacteria in our mouths used to be more diverse. Well-preserved microbiomes from 4,000-year-old teeth in a limestone cave showed modern humans are losing microbial diversity, according to a new study.

The old teeth samples housed a higher diversity of a strain of Tannerella forsythia — a bacteria involved in gum disease — compared to modern humans, the study published in journal Molecular Biology and Evolution noted.


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“These strains from a single ancient mouth were more genetically different from one another than any pair of modern strains in our dataset, despite these modern samples deriving from Europe, Japan, and the United States. The two sampled teeth contained quite divergent strains of Tannerella forsythia,” Iseult Jackson, a PhD candidate and first author of the study, said in a statement.

This, she added, is because a loss of biodiversity can have negative impacts on the oral environment and human health.

The new study also adds to data on how human oral microbiome evolved over time. Currently, three quarters of published ancient oral metagenomes are from within the last 2,500 years, with few full genomes available from prior to the medieval period.

At present, researchers have limited knowledge about prehistoric bacterial diversity and how they have responded to recent dietary changes such as the expansion of farming, which began about 10,000 years ago. Ancient human teeth could also provide information on how the oral microbiome has evolved over the years.

In this new study, researchers recovered bacterial genomes from teeth that were found among a large assemblage of skeletal remains excavated from a limestone cave in Killuragh, County Limerick, Ireland.

The team found no evidence of dental caries on the sampled teeth, while one tooth root yielded a high quantity of sequences of Streptococcus mutans — bacteria involved in causing decay.


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From this individual, the team retrieved the first ancient Streptococcus mutans genome and two distinct strains of Tannerella forsythia. They also found that the two species have experienced dramatic changes over the last 750 years.

“We were very surprised to see such a large abundance of mutans in this 4,000-year-old tooth,” Lara Cassidy, an assistant professor at Trinity College Dublin and senior author of the study, said in a statement. 

This, she added, suggests this man was at high risk of developing cavities right before his death.

However, the team did not find other streptococcal species. This, according to the paper, suggested that Streptococcus mutans had outcompeted the other species, leading to a pre-disease state.

Their success and expansion have been tied to the increased popularity of sugar. “Streptococcal mutans are very adept at swapping genetic material across strains,” Cassidy explained, adding that the swapping would enable an advantageous innovation to be spread across mutans lineages, rather than one lineage becoming dominant and replacing all others.


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On the other hand, only one lineage of Tannerella forsythia dominates globally currently, suggesting that one strain, in particular, has some genetic advantage over the others

Since the industrial era, the team pointed out, Tannerella forsythia genomes have acquired many new genes that help it colonise the oral environment and cause disease.

This finding supports the theory of the disappearing microbiome, which proposes that the microbiomes of our ancestors were more diverse than our own today and this loss of diversity could lead to chronic diseases.




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