MetaBear: Understanding interactions of the microbiome and host genomics in a wild bear population through a temporal hologenomics approach

Symbiotic microbiomes play a central role in many biological processes and are intrinsically linked to host health. The composition of host-associated microbiomes is mediated by host genetics, which is particularly relevant to wild systems in the face of global climate change and rapid population declines. It is thus crucial to understand how changes in genetic diversity impact host-microbiome interactions. Achieving this goal in wild populations requires samples that span decades-centuries of population declines, yet host-associated microbiomes often do not preserve after host death. To address this significant knowledge gap, we will utilise dental calculus, the calcified oral microbiome, from museum-preserved specimens of

Scandinavian brown bears that experienced a dramatic population bottleneck over the course of the last 200 years. Preliminary research in our group found an inverse relationship between the prevalence of dental caries (cavities resulting from tooth decay) and population size. The main research objectives of MetaBear are to investigate i) the role of host population genomics in the prevalence of oral disease, ii) how population declines and host genetics shape oral microbiomes, and iii) the evolution of oral pathogens and emergence of virulence factors. In a world first, we will integrate state-of-the-art ancient DNA techniques with metagenomics, population genomics and phylogenomics to establish a new field of research - Temporal Hologenomics, the study of hosts and microbiomes over time. Insights from MetaBear are intrinsically interdisciplinary and will have direct applications to conservation and evolutionary biology, as well as EU Green Deal and UN Sustainable Development Goals strategies. The open-access Temporal Hologenomic bioinformatic pipelines developed in this project will be taught in dedicated workshops, enhancing the uptake of this approach in evolutionary, clinical and conservation biology.