The microbiome is essential to mediate the health of animals, modulating various physiological processes such as digestion, immune function, and metabolism. The review discusses recent advances and future directions in our understanding of microbiomes as modulators for animal health and disease, specifically targeting the contributions made by gut microbiota. Dysbiosis, denoting microbial imbalance in association with various animal diseases such as gut disorders, metabolic syndromes, and immune dysregulation. New microbiome-based interventions, including probiotics, prebiotics, and fecal microbiota transplantation (FMT), emerge with the potential to benefit animal health by repopulating the gut ecology. Yet, many challenges remain in characterizing the diversity of animal microbiomes and how their composition reflects species- or environment-specific dynamics as well as changes associated with different health states. The review also suggests emerging trends in microbiome research and the importance of using precision medicine strategies based on species-level microbiota profiles. Recent research shows that in the future, microbiome science will change animal health management after huge breakthroughs were achieved as a result of improvements on both sequencing technologies and bioinformatics tools. Knowledge of the complex interplay between microbiomes and their animal host counterparts will be paramount for future advances in targeted therapeutics to better strengthen health outcomes and ultimately prevent disease. In both cases, the potential to attach microbiome-based solutions is set to advance animal health in light of increasing concerns over antimicrobial resistance and sustainable animal agriculture.