Herbivorous animals rely on complex gastrointestinal systems and microbial communities to efficiently digest plant-based diets, extract nutrients, and maintain health. Recent advances in metagenomic technologies have enabled high-resolution, culture-independent analysis of gut microbiota composition, functional potential, and host–microbe interactions, providing insights into microbial diversity across the herbivore digestive tract. This review summarizes key findings on the gastrointestinal microbiota of herbivores, focusing on ruminant foregut and non-ruminant hindgut fermentation. Ruminants like cattle, sheep, and goats host microbiota enriched with fibrolytic and methanogenic microbes that facilitate fiber degradation and volatile fatty acid production, contributing significantly to energy balance. In contrast, non-ruminants such as horses and rabbits rely on hindgut fermentation, with distinct microbial taxa contributing to carbohydrate and protein breakdown. The review further explores how specific microbial taxa, including Prevotella, Fibrobacter, and Ruminococcus, correlate with improved feed efficiency and growth performance, particularly in ruminants. Additionally, the roles of probiotics, prebiotics, and symbiotics in modulating gut microbial composition and enhancing productivity are discussed. Despite significant advances, challenges remain in microbial sampling, functional annotation, and understanding the integration of microbiota with host physiology. The review emphasizes the potential of metagenomic insights in optimizing herbivore gut microbiota to improve feed efficiency, health, and sustainable livestock production.

Donkeys (Equus asinus) remain nutritionally understudied despite their critical roles in agriculture across developing regions, with current feeding practices inappropriately extrapolating horse standards without accounting for species-specific digestive physiology. No comprehensive synthesis has integrated how dietary modifications systematically alter gut microbial communities to drive measurable health outcomes in donkeys, preventing development of evidence-based feeding strategies. This review critically synthesizes current evidence on donkey nutritional requirements and gut microbiota dynamics to establish mechanistic frameworks for optimizing health and productivity. Donkeys exhibit remarkable adaptations including 30% superior fiber digestibility versus horses and specialized hindgut fermentation where microbiota provide 60–70% of metabolic energy. Targeted nutritional interventions—protein supplementation (12.52%), methionine supplementation (5–15 g/day), and optimized energy levels (10.49 MJ/kg)—have shown preliminary evidence of modulating beneficial microbial populations (Prevotella, Ruminococcus, Akkermansia, Bacteroides), with short-term studies (typically 30–60 days, n < 10 animals) indicating potential reducing oxidative stress (20–40%), decreasing inflammatory cytokines (30–50%), and improving growth performance (15–25%). However, these findings require validation through larger-scale, longer-term studies to establish sustainable effects and broader applicability. Non-conventional feeds including reed silage, bamboo leaves, and garlic byproducts offer sustainable alternatives. This narrative review uniquely establishes mechanistic pathways linking dietary modifications to microbiota changes and downstream physiological effects, providing the first comprehensive framework integrating digestive physiology, microbiota ecology, and nutritional interventions specifically for donkeys to support evidence-based, sustainable feeding strategies.