Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from...

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Autores principales: Ottoni, Claudio, Borić, Dušan, Cheronet, Olivia, Sparacello, Vitale, Dori, Irene, Coppa, Alfredo, Antonović, Dragana, Vujević, Dario, Price, T. Douglas, Pinhasi, Ron, Cristiani, Emanuela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2021
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8364157/
https://www.ncbi.nlm.nih.gov/pubmed/34312252
http://dx.doi.org/10.1073/pnas.2102116118
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author Ottoni, Claudio
Borić, Dušan
Cheronet, Olivia
Sparacello, Vitale
Dori, Irene
Coppa, Alfredo
Antonović, Dragana
Vujević, Dario
Price, T. Douglas
Pinhasi, Ron
Cristiani, Emanuela
author_facet Ottoni, Claudio
Borić, Dušan
Cheronet, Olivia
Sparacello, Vitale
Dori, Irene
Coppa, Alfredo
Antonović, Dragana
Vujević, Dario
Price, T. Douglas
Pinhasi, Ron
Cristiani, Emanuela
author_sort Ottoni, Claudio
collection PubMed
description Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe—the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.
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spelling pubmed-83641572021-08-24 Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus Ottoni, Claudio Borić, Dušan Cheronet, Olivia Sparacello, Vitale Dori, Irene Coppa, Alfredo Antonović, Dragana Vujević, Dario Price, T. Douglas Pinhasi, Ron Cristiani, Emanuela Proc Natl Acad Sci U S A Biological Sciences Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe—the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent. National Academy of Sciences 2021-08-10 2021-07-26 /pmc/articles/PMC8364157/ /pubmed/34312252 http://dx.doi.org/10.1073/pnas.2102116118 Text en Copyright © 2021 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Biological Sciences
Ottoni, Claudio
Borić, Dušan
Cheronet, Olivia
Sparacello, Vitale
Dori, Irene
Coppa, Alfredo
Antonović, Dragana
Vujević, Dario
Price, T. Douglas
Pinhasi, Ron
Cristiani, Emanuela
Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus
title Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus
title_full Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus
title_fullStr Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus
title_full_unstemmed Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus
title_short Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus
title_sort tracking the transition to agriculture in southern europe through ancient dna analysis of dental calculus
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8364157/
https://www.ncbi.nlm.nih.gov/pubmed/34312252
http://dx.doi.org/10.1073/pnas.2102116118
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