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Ancient Plaque Provides Clues to Diet's Effects on Human Mouth Microbiome

NEW YORK (GenomeWeb News) – Dental disease-causing bacteria rose through the ranks of mouth microbiomes as humans transitioned from hunter-gather diets to a diet centered around agriculture and again, more recently, as human diets began including processed foods, according to a new Nature Genetics study.

A research team from Australia, the UK, and Germany used 16S ribosomal RNA gene sequencing to characterize microbial communities in dental plaque samples from nearly three-dozen human skeletons. These individuals all came from Europe and died between a few hundred and nearly 10,000 years ago.

Compared to the microbial mouth communities in present day samples, the earliest oral microbiomes tested — those from hunter-gatherers living during the Mesolithic period — tended to harbor fewer species associated with tooth decay such as Streptococcus mutans and Porphyromonas gingivalis, the investigators reported.

Their results suggest that oral microbiomes started to change during the Stone Age with the introduction of an agricultural diet. Another shift appears to have occurred sometime after medieval times, leaving microbe communities in the modern mouth less varied than they were prior to the Industrial Revolution in Europe.

"The composition of oral bacteria changed markedly with the introduction of farming, and again around 150 years ago," explained corresponding author Alan Cooper, who directs the University of Adelaide's Centre for Ancient DNA, in a statement.

"With the introduction of processed sugar and flour in the Industrial Revolution, we can see a dramatically decreased diversity in our oral bacteria, allowing domination by caries-causing strains," he continued, suggesting the "modern mouth basically exists in a permanent disease state."

Because bacteria-containing dental plaque biofilms can eventually mineralize into a "dental calculus" that sticks to teeth, the study's authors noted, mining the genetic material in this hardened plaque provides a peek at the microbes that once lived in an individual's teeth — even many years after death.

"Calculus represents one of the few sources of preserved human and hominid microbiota," they wrote, "and genetic analysis has the potential to create a powerful record of dietary impacts, health changes, and oral pathogen genomic evolution deep in the past."

For their current analysis, the investigators relied on dental calculus samples nicked from the skeletal remains of 34 Europeans who lived as long as 7,550 years ago. Together, these represented individuals from Mesolithic (hunter-gatherer), Neolithic (early agricultural), and Bronze Age societies, as well as individuals living in rural and urban environments during medieval times.

The team also tested plaque and calculus samples from modern-day individuals of European descent using Roche 454 GS FLX Titanium sequencing to profile hyper-variable 16S rRNA gene amplicons from each of the contemporary and ancient samples.

Along with the 16S sequencing, which offered a general look at the organisms present in each oral microbiome, the researchers did targeted testing for two pathogens: S. mutans and P. gingivalis. To help weed out potential contaminants coming from microbes that moved into the teeth after death, meanwhile, they sequenced 16S amplicons from ancient tooth samples as well.

When the group sorted through this sequence data, it saw representatives from the same main microbial phyla turning up in mouth microbial communities stretching across the time periods and individuals tested.

But there were differences, too. For instance, oral microbial communities in the hunter-gatherers from the Mesolithic Age had higher diversity than microbiomes in the mouths of those living during the Stone Age, when cereal crop consumption and other forms of agriculture started to increase.

The Stone Age samples also contained more of the cavity-associated pathogenic bacteria, a pattern that continued in samples from the Bronze Age and medieval individuals.

Mouth microbiomes seem to have lost diversity again — while seeing a rise in S. mutans levels — in the years following the Industrial Revolution, researchers noted.

"This is the first record of how our evolution over the last 7,500 years has impacted the bacteria we carry with us, and the important health consequences," Cooper said. "Oral bacteria in modern man are markedly less diverse than historic populations," he continued, "and this is thought to contribute to chronic oral and other disease in post-industrial lifestyles."

Going forward, the team plans to take the ancient plaque-based approach used for the current analysis and apply it to more samples from humans and other hominins (such as Neandertals) to get a more complete picture of the oral microbiome relative to time, diet, host species, and so on.

"Our research has identified a powerful new avenue for bioanthropological research," Cooper and his co-authors concluded, "which promises to provide the first detailed genetic records of the evolution of human microbiota."

The team noted, too, that ancient oral microbiome data could prove useful for learning more about population structure, migration, and admixture, since certain features of oral microbiome development and maintenance are thought to be influenced by family members.

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