The gut microbiome has emerged as a central determinant of health, metabolism, immune competence, and disease outcomes in companion animals, playing a critical role in maintaining overall physiological balance. Advances in high-throughput sequencing technologies, metagenomics, and metabolomics have revealed highly diverse and complex microbial ecosystems in dogs and cats that interact dynamically with dietary inputs, host genetics, age, lifestyle, and environmental factors. These microbial communities influence nutrient digestion, bioavailability, short-chain fatty acid production, inflammatory pathways, and systemic metabolic regulation.

This review synthesizes current scientific evidence linking the gut microbiome to nutrient metabolism, immune modulation, gastrointestinal function, metabolic disorders, obesity, and functional dietary responses in pets. We discuss the mechanisms through which diet composition, ingredient quality, and feeding strategies shape microbial diversity, stability, and metabolic activity. In addition, we evaluate the role of emerging functional ingredients—including prebiotics, probiotics, postbiotics, synbiotics, and fermented components—in modulating gut health. Personalized nutrition strategies based on microbiome profiling are also explored. Finally, we identify research gaps and future directions for integrating microbiome science into innovative pet food formulation and clinical veterinary practice.