Building on the foundational concepts of Fecal Microbiota Transplantation (FMT), this advanced session focuses on the practical implementation and future innovations of microbiome-based therapies in veterinary medicine. The lecture will provide a detailed framework for FMT donor selection and screening, outlining best practices for pathogen and parasite testing, medical history evaluation, and microbiome profiling. Attendees will learn when and how to incorporate microbiome testing in clinical decision-making, with case-based applications for conditions beyond gastrointestinal disease, including Atopic Dermatitis and neurological disorders. The session will also cover advanced FMT administration techniques, including nasal-jejunal tubes, endoscopy, rectal enemas, and oral capsules, with a focus on dosing strategies, treatment protocols, and patient monitoring. Finally, we will explore cutting-edge research in microbiome-based therapeutics, such as synthetic microbiota, precision probiotics, and personalized microbial formulations, discussing how these advancements may reduce reliance on traditional FMT in the future. This session is designed for veterinarians who want to move beyond the basics and gain practical expertise in microbiome modulation for clinical practice.