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.

Equines play a crucial role in global food security, economic development, and recreation, particularly in regions such as Central Asia, parts of Africa, and South America. However, parasitic infections significantly impact their health, productivity, and reproductive performance, leading to economic losses and reduced animal welfare. This review synthesizes the effects of parasitic infections, including protozoan, helminthic, and ectoparasitic species, on equines. These infections cause hematological alterations like anemia, leukocytosis, leukopenia, and thrombocytopenia, compromising overall health and resilience. Protozoan parasites, such as Trypanosoma spp., Theileria equi, and Babesia caballi, directly affect semen quality and fertility by causing testicular lesions, orchitis, and hormonal disruptions. Helminths like Cyathostomins and Strongyles reduce nutrient absorption, impairing productivity, while some protozoan species can cause abortion through transplacental transmission. Zoonotic parasites, including Sarcocystis spp. and Toxoplasma gondii, pose a human health risk through contaminated meat and milk consumption. Despite the effectiveness of conventional anthelmintics, emerging biological control methods like Duddingtonia flagrans (BioWorma^® and Bioverm^®) show promise. However, the development of standardized herbal anthelmintics and vaccines is hindered by limited efficacy validation, complex parasite biology, and inadequate funding. The need for better diagnostic tools and sustainable treatments remains critical for the long-term sustainability of the equine industry.

Donkeys (Equus asinus) are economically and ecologically important livestock species whose genetic potential remains underexplored. This review synthesizes recent advances in donkey genomics, tracing their evolutionary history while evaluating current applications in selective breeding, conservation genetics, and agricultural management. By integrating evidence from population genomics, functional genomics, and comparative evolutionary studies, we summarize major genomic discoveries and identify persistent knowledge gaps, with a focus on translating genomic information into practical breeding outcomes. High-quality reference genomes, population resequencing, and ancient DNA analyses have clarified the African origin, global dispersal history, and environmental adaptation of donkeys. Genome-wide approaches, including GWAS, QTL mapping, and multi-omics analyses, have further identified genes and regulatory pathways associated with thermotolerance, metabolism, reproduction, and milk production. Nevertheless, progress is still limited by small sample sizes, variable sequencing depth, and inconsistencies in phenotyping and bioinformatic pipelines, which constrain cross-population comparisons and practical applications. Addressing these challenges through standardized phenotyping, improved data integration, and collaborative research frameworks will lay the groundwork for effective conservation strategies and sustainable genomic breeding of global donkey populations.