The Expanding Landscape of Microbiota Medicine: Indications, Therapeutic Modalities, and the Path Towards Integrative Microbiome‐Targeting Healthcare

ABSTRACT The growing recognition of the microbiome's role in human health has propelled the emergence of microbiota medicine—a new discipline integrating microbiology, multi‐omics, and clinical science. Advances in sequencing, data integration, and interventions such as fecal microbiota transplantation (FMT) have transitioned the field from observational association towards therapeutic exploration across a spectrum of diseases. However, key challenges remain in establishing causal mechanisms, ensuring reproducible biomarkers, and bridging the efficacy gap between FMT for recurrent Clostridioides difficile infection (CDI) and other complex disorders. The trajectory of microbiota medicine points towards its maturation into a structured clinical discipline, moving from broad ecological modulation towards targeted, mechanism‐based interventions that require interdisciplinary collaboration and robust translational frameworks. This review aims to provide a comprehensive overview of recent advances in microbiota medicine, spanning from its indications, therapeutic modalities, and diagnostic evidence to the disciplinary challenges and future prospects that will shape the field.