Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

bicicleur 2

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[h=2]Abstract[/h]The human microbiome has recently become a valuable source of information about host life and health. To date little is known about how it may have evolved during key phases along our history, such as the Neolithic transition towards agriculture. Here, we shed light on the evolution experienced by the oral microbiome during this transition, comparing Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers that populated a same restricted area in Italy. We integrate the analysis of 76 dental calculus oral microbiomes with the dietary information derived from the identification of embedded plant remains. We detect a stronger deviation from the hunter-gatherer microbiome composition in the last part of the Neolithic, while to a lesser extent in the early phases of the transition. Our findings demonstrate that the introduction of agriculture affected host microbiome, supporting the hypothesis of a gradual transition within the investigated populations.

In conclusion, our analysis provides evidence for the presence of two main shifts affecting the abundance of several species of oral microbiome in the investigated populations: (i) the first is related to the cultural transition associated with the introduction of the agricultural lifestyle in this region, which drove an initial modification in the microbiome composition while retaining some aspects of the previous hunter-gatherer samples; (ii) the second, occurred during the late Neolithic, and is probably linked to the adaptation to distinct dietary elements, when the changes observed in the first phase became more prominent and some species that were strongly present in the hunter-gatherers almost disappeared, probably due to the progressive adaptation of farmers to distinct dietary elements.


This paper by stating, "The microbiomes of the analysed hunter-gatherer individuals [Paglicci Cave, 31,000–11,000 BC]" are highly similar, despite belonging to a long chronological period that encompasses the last glacial maximum, and possibly a population replacement in the subsequent period", contradicts the paper by Johannes Krause and others (May 2021), "The evolution and changing ecology of the African hominid oral microbiome" that using 20 oral microbiomes of hunter-gatherers Sapiens and 17 de Neanderthals since 100,000 years, concludes " the oral taxa of [european] individuals dated to before 14 ka mostly falling with Neanderthals and those after 14 ka mostly clustering with present-day modern humans."

The paper by Johannes Krause and others stated this forgetting that none of the 20 Sapiens they analyzed are from Italy or the Balkan Peninsula and of the 17 Neanderthals, only one is from northern Italy and another from the northern Balkan Peninsula.

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