Seasonal dynamics of Alpine ibex (Capra ibex) gut microbiome in the Central Italian Alps
In order to increase our knowledge of the biology of the gut microbiome of wild ruminants, also in terms of its possible exploitation in lignocellulose bioconversion processes, here we apply multiomic techniques to characterize the seasonal dynamics of the gut microbiome of the Alpine ibex (Capra ibex) within the Stelvio National Park, Central Italian Alps. Fecal samples were collected from 86 wild individuals across 3 different seasons (spring, summer and fall) during 2-3-day non-invasive samplings. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that allow the host to adapt to seasonal changes in available forage, by fine-tuning the catabolic layout at the holobiont level to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the necessary phenotypic plasticity to buffer dietary changes, by obtaining species-level genome bins from the ibex gut microbiome, we identified minimal community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulosic biomasses to high-value compounds, such as volatile fatty acids.