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Ancient Human Dietary Changes Detected Using Plaque Microbe Analyses

NEW YORK – An Italian research team retraced dietary shifts in Paleolithic, Neolithic, and Copper Age individuals in central and southern Italy — including oral microbiome community shifts accompanying the transition from hunter-gatherer to farming lifestyle and subsequent dietary adaptations — by analyzing microbial DNA in dozens of ancient plaque samples.

"Our findings demonstrate that the introduction of agriculture affected [the] host microbiome, supporting the hypothesis of a gradual transition within the investigated populations," co-first and co-corresponding authors Andrea Quagliariello, a comparative biomedicine and food science researcher at the University of Padua, and Alessandra Modi, a biology researcher at the University of Florence, and their colleagues wrote in Nature Communications on Tuesday.

Using metagenomic sequencing, a differential expression clustering method called DESeq2, microscopic profiling, and network analyses, the researchers profiled microbial community members in 76 dental calculus samples, including nine samples from the mouths of Upper Paleolithic hunter-gatherers found in the Paglicci Cave and 67 plaque samples from individuals spanning the hunter-gatherer-to-farming transition and other points in the Neolithic period or from post-Neolithic farming representatives from the Copper Age.

The team's results pointed to two oral microbiome shifts uncovered with sequence clusters in the ancient plaque samples. The microbial community membership changes appeared to be relatively subtle during early stages of the hunter-gatherer-to-farming transition that occurred roughly 8,200 years ago compared to more pronounced oral microbiome community shifts that took place later in the Neolithic.

"The first modification occurred between local hunter-gatherer communities and Neolithic farmers, while a second unexpected major change was identified in the last part of the Neolithic period," the authors reported, noting that "[s]ome of the taxonomic and functional changes were probably driven by changes in subsistence strategies."

The investigators flagged five clusters of microbial species in the dental calculus samples considered, including a cluster that characterized the Paleolithic hunter-gatherer samples. Certain species with pronounced representation in samples from the Paleolithic — including Actinomyces and Streptococcus species — declined in the dental calculus samples from time points after the early Neolithic hunter-gatherer-to-farming transition.

Along with apparent changes involving carbohydrate metabolism, vitamin metabolism, virulence, and other microbial functions in the oral microbe communities, the team saw a Neolithic period rise in representation by some Campylobacter and Capnocytophaga species, Porphyromonas gingivalis, and other microbes that were relatively rare in the Paleolithic plaque.

Together with other data, the genetic results suggested that "transition to the new subsistence strategy was gradual and regionally specific, with a strong adaptation of the arriving Neolithic people to locally available resources, instead of a drastic change to a homogenous diet," the authors reported, noting that "during the second half of the Neolithic period, multiple taxonomic and functional traits led us to suppose the adoption of a high-carbohydrate/low-protein dietary regimen."