Gut bacterial and fungal microbiome of donkeys under permanent and regenerative grazing systems
This BioProject comprises high-throughput amplicon sequencing data generated to investigate the effects of grazing management on the gut microbiome of donkeys (Equus africanus asinus) managed under extensive pasture conditions. Fecal samples were collected from donkeys maintained under two contrasting grazing systems, permanent grazing and regenerative grazing, at two sampling time points (start and end of the grazing period).Bacterial community composition was characterized by sequencing the V3-V4 region of the 16S rRNA gene, while fungal community composition was assessed using ITS region amplicon sequencing. The project aims to compare bacterial and fungal gut microbial community structure, diversity, and differential abundance between grazing systems and over time, with a particular focus on abundance-driven community restructuring and the response of anaerobic gut-associated fungi.The generated sequence data provide a resource for understanding how grazing management influences gut microbial ecology in hindgut-fermenting herbivores under extensive grazing regimes and contribute to the limited available data on donkey gut microbiomes, particularly with respect to fungal communities.