Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave

Abstract

Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.

Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes

“…Interestingly, diseased modern samples were characterized by increased Gram-negative, anaerobic bacteria. The ancient samples exhibited similar characteristics, hinting at the possibility of dental disease for those ancient individuals [147]. These findings are contradicted by Velsko et al [141], who found that there were no patterns linking a state of dental disease with changes in the composition or function of the oral microbiomes of smokers and non-smokers in post-Medieval Netherlands.…”

A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review

“…After perusing the full-text versions, 19 articles were selected for the purpose of framing the scoping review (Table 1). They were published between 2013 and 2023 [7,21,22,24,[37][38][39][40][41][42][43][44][45][46][47][48][49][50]. No data emerged about the age of the ancient population sampled, except for one study reporting data on a juvenile mandible [47], and others clarified that the ancient population was of adult age [46,49].…”

“…A study does not specify the samples' geographical origin [40]. The human remains herein taken into account range from 6000 years ago to the 19th century [7,21,22,24,26,[37][38][39][40][41][42][43][44][45][46][47][48][49][50].…”

Bioarchaeological and paleogenomic profiling of the unusual Neolithic burial from Grotta di Pietra Sant’Angelo (Calabria, Italy)

“…Four microliters of the sample/control were injected. LC and MS parameters were run according to the dental calculus method in Scorrano et al 102 , with the HCD collision energy at 30%, RF Lens at 40%, and MS2 inject time of 54 ms to adjust for differences between the mass spectrometers.…”