Background Dental 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). Results 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 are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. Conclusions We 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.

SummaryThe history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.

In Early Middle Ages (sixth-eleventh centuries AD), South Tyrol (Italian Alps) played a key role for geographical and military reasons. Historical sources document that allochthonous groups (germani) entered the territory, and the material culture shows mutual cultural exchanges between autochthonous and germani. Besides the nature of the migration, the demographic and socio-cultural impacts on the local population are still unknown. Stable isotope analyses were performed to provide insights into dietary patterns, subsistence strategies, changes in socio-economic structures, and mobility, according to spatial (e.g. valleys, altitudes) and chronological (centuries) parameters. Bone collagen of 32 faunal and 91 human bone samples from nine sites, located at different altitudes, was extracted for stable carbon, nitrogen, and sulphur isotope analyses. In total, 94% (30/32) of the faunal remains were of good quality, while the humans displayed 93% (85/91) of good quality samples for δ 13 C and δ 15 N and 44% (40/91) for δ 34 S stable isotopes. The isotopic results of the animals reflected a terrestrial-based diet. Statistical differences were observed within and among the humans of the different valleys. The δ 13 C values of individuals sampled from higher altitudes indicated a mainly C 3 plant-based diet compared to areas at lower altitudes, where more positive δ 13 C values showed an intake of C 4 plants. The δ 15 N values suggested a terrestrial-based diet with a greater consumption of animal proteins at higher altitudes. The data revealed higher variability in δ 34 S values in the Adige valley, with individuals probably migrating and/or changing dietary habits.

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