Metagenomic analysis reveals shared and distinguishing features in horse and donkey gut microbiome and maternal resemblance of the microbiota in hybrid equids

Mammalian gut microbiomes are essential for host functions like digestion, immunity, and nutrient utilization. This study examines the gut microbiome of horses, donkeys, and their hybrids, mules and hinnies, to explore the role of microbiomes in hybrid vigor. We performed whole-genome sequencing on rectal microbiota from 18 equids, generating detailed microbiome assemblies. Our analysis revealed significant differences between horse and donkey microbiomes, with hybrids showing a pronounced maternal resemblance. Notably, Firmicutes were more abundant in the horse-maternal group, while Fibrobacteres were richer in the donkey-maternal group, indicating distinct digestive processes. Functional annotations indicated metabolic differences, such as protein synthesis in horses and energy metabolism in donkeys. Machine learning predictions of probiotic species highlighted potential health benefits for each maternal group. This study provides a high-resolution view of the equid gut microbiome, revealing significant taxonomic and metabolic differences influenced by maternal lineage, and offers insights into microbial contributions to hybrid vigor.