Gut microbiome seasonality is associated with dietary plasticity and coexistence in three sympatric Pamir ungulates

This graphical abstract outlines a multi-omics framework investigating the seasonal dietary composition and gut microbial communities of three coexisting ungulate species inhabiting the extreme high-altitude Pamir Plateau (Ovis ammon polii, Capra sibirica, and Pseudois nayaur). By integrating dietary DNA metabarcoding, 16S rRNA gene sequencing, shotgun metagenomics, and untargeted metabolomics across winter and summer, we explored how seasonal nutritional bottlenecks influence host–microbiome interactions. Our results reveal a pronounced seasonal restructuring of gut microbial communities, co-varying with interspecific dietary niche differentiation. Importantly, we demonstrate that seasonal environmental filtering and host dietary strategies are jointly linked to microbial functional potential (e.g., energy harvest and detoxification). These functional shifts are reflected by corresponding alterations in the gut metabolome, providing comprehensive biochemical evidence for microbiome-associated nutritional adaptation.