Fecal microbiota transplantation in adolescents with obesity induces limited and donor-dependent remodeling of the gut microbiome

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Introduction Obesity is a global health challenge, and fecal microbiota transplantation (FMT) is considered a potential intervention; however, its long-term ecological impact remains unclear. Methods In this 182-day longitudinal cohort of adolescents with obesity (378 samples), metagenomic sequencing was used to assess FMT-induced remodeling of the multi-kingdom gut ecosystem through species composition, diversity, microbial networks, and machine learning analyses. Results FMT induced only transient shifts in community structure, with limited donor strain engraftment and strong resilience of recipient core taxa. Bacteria were the primary responders, the virome showed short-term perturbation, and network restoration was partial and donor-dependent. Discussion FMT exerts limited, donor-dependent ecological effects in obese adolescents. Optimizing donor selection and personalized matching may be essential for improving long-term efficacy.