Seasonal and Species-Specific Variations in Gut Microbiota of Wild Ungulates in Captivity

Seasonal variation can strongly restructure the gut microbiota of herbivores, but under captive conditions it remains unclear whether these shifts outweigh host-species effects when diet is standardized. Here, we profiled the gut microbiota of captive mouflon, argali, and blue sheep in summer and winter using 16S rRNA amplicon sequencing, ASV-based compositional beta-diversity analysis, ANCOM-BC2, and PICRUSt2 functional prediction. Across hosts, Chao1 richness decreased in winter, whereas Shannon diversity remained comparatively stable, indicating that seasonal change affected richness more strongly than evenness. CLR-based ordination further showed that the three species were relatively close in summer but became more clearly separated in winter, especially mouflon and blue sheep, consistent with pronounced seasonal restructuring under a common diet. At the phylum level, summer communities were broadly similar and dominated by Firmicutes_A and Bacteroidota, whereas winter brought stronger taxonomic shifts in mouflon and blue sheep, including marked increases in Proteobacteria and Firmicutes_D. Argali showed a narrower and taxonomically different seasonal response. Genus-level analyses similarly indicated that winter restructuring was host-dependent rather than uniform, with winter-associated enrichment of several Bacillales/Planococcaceae-related lineages and Proteobacteria-associated taxa, particularly in mouflon and blue sheep. Predicted functional profiles inferred by PICRUSt2 also shifted between summer and winter within each host species, suggesting that seasonal restructuring extended beyond taxonomy, although these results should be interpreted as inferred functional potential rather than direct metabolic activity. Overall, our findings support seasonality as the primary axis of gut microbiota variation in captivity, while the host species modulates the magnitude and taxonomic features of these seasonal changes. These results highlight the need to consider seasonal effects in captive management and provide a basis for future multi-omics validation of host-microbiome interactions in wild ungulates.