Abstract
Dental calculus (mineralized dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus is thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterized 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). We 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 were prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. Our study suggests that some members of the pre-industrial human oral microbiome such as the newly discovered archaeal species are now rare in the modern human oral microbiome.