Permanent and Regenerative Grazing Systems Are Associated with Distinct Fecal Bacterial and Fungal Microbiota Patterns in Donkeys Under Extensive Pasture Conditions

This study investigated whether permanent and regenerative (rotational) grazing systems are associated with differences in fecal bacterial and fungal microbiota of donkeys under extensive pasture conditions. Young female donkeys were assigned to permanent or regenerative grazing, and paired fecal samples from eight animals per system were collected before pasture access and at the end of the grazing period. Culture-based microbial counts, parasitological examination, animal performance measurements, forage assessment, and bacterial 16S rRNA gene and fungal ITS amplicon sequencing were performed. Donkeys under regenerative grazing showed higher average daily gain than those under permanent grazing (378.0 ± 57.8 vs. 242.4 ± 65.8 g/day; p < 0.001), whereas culture-based fecal microbial counts and fecal egg counts did not differ significantly between systems. Beta-diversity analyses identified sampling time as a consistent source of variation in both bacterial and fungal communities, whereas associations with grazing system and its interaction with sampling time depended on the distance metric used. Bacterial communities retained a large shared core, whereas fungal communities showed stronger compositional turnover. Longitudinal differential abundance analysis identified 336 bacterial and 66 fungal amplicon sequence variants (ASVs) with significant grazing system × sampling time interactions. More positive temporal responses under regenerative grazing were observed among several Spirochaetota and Neocallimastigomycota ASVs, whereas detected Methanobrevibacter ASVs showed a more positive temporal change under permanent grazing.