Abstract
BackgroundDental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000–3500 BCE) to the Early Middle Ages (400–1000 CE).ResultsWe found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods.ConclusionsWe have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia.8LjH7Wn3nngikkNWL3zB9VVideo abstract
Highlights
Dental calculus preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are an important source of information regarding our ancestral human oral microbiome
Methanobrevibacter oralis is the only isolated and characterised Methanobrevibacter species in the human oral microbiome [15], but undetermined Methanobrevibacter species have been continuously found in ancient dental calculus [6, 11, 14, 16] in as high abundances as >60% [14, 17]
Periodontitis was evaluated to be present or absent, where it was present if the distance between the cemento-enamel junction (CEJ) and the margin of the Sampling, DNA extraction and sequencing All genetic laboratory work was conducted in the dedicated ancient DNA lab of the Institute for Mummy Studies at Eurac Research, Bolzano, Italy
Summary
Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are an important source of information regarding our ancestral human oral microbiome. Dental calculus develops via the mineralisation of plaque, which can remain for millennia on ancient skeletal remains It displays a specific microniche in the oral cavity and has been shown to perfectly preserve ancient biomolecules (DNA, proteins, metabolites) [1,2,3] and Granehäll et al Microbiome (2021) 9:197 bacteria highly associated with periodontal disease [8], as well as the presence of inflammatory host response proteins [5, 9,10,11,12,13,14]. Despite the high abundance of Methanobrevibacter spp. in ancient dental calculus and its possible involvement in periodontal disease [18, 19], the current knowledge on the diversity and role of these methanogens in the human oral microbiome is limited
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