The gut microbiome plays a pivotal role in athletic health and performance by influencing metabolism, immunity, gastrointestinal integrity, and recovery. Advances in high-throughput sequencing and integrative multi-omics approaches have provided unprecedented insights into how microbial communities adapt to the physiological demands of training and competition. Key microbial taxa, including short-chain fatty acid producers, lactate utilizers, and carbohydrate fermenters, have been linked to enhanced endurance, reduced inflammation, and improved recovery, opening exciting opportunities for targeted probiotic interventions. While conventional probiotics remain valuable, next-generation engineered strains hold particular promise, supported by recent regulatory milestones such as FDA approvals of engineered probiotics and gene-edited livestock. In this narrative review, we synthesize recent multi-omics research to examine mechanistic links between the athlete gut microbiome and performance, evaluate current and emerging probiotic strategies, and highlight challenges related to personalization, standardization, and regulation. With longitudinal, performance-oriented trials and harmonized frameworks, microbiome-targeted interventions are poised to move beyond exploratory research toward evidence-based, precision tools that optimize athletic performance and recovery.