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Background: Fecal Microbiota Transplantation (FMT) is a therapeutic intervention involving the transfer of gut microbiota from healthy donors to individuals with dysbiosis, with the aim of restoring microbial homeostasis. Its efficacy is well established for the treatment of recurrent Clostridioides difficile infection. However, evidence supporting its use in small intestinal bacterial overgrowth (SIBO), particularly in patients who have undergone bariatric surgery, remains limited. Studies report that the prevalence of bacterial overgrowth after Roux-en-Y gastric bypass ranges from 29% to 53%, depending on the duration of postoperative follow-up. This study reports a clinical experience addressing this gap. Objectives: It was to report the clinical experience of FMT in a post– Roux-en-Y gastric bypass patient with SIBO and to develop an institutional FMT protocol for future clinical application. Methods: This prospective, open-label clinical experience was approved by the Research Ethics Committee of a tertiary care hospital, Fundação Hospital Adriano Jorge (FHAJ), under number 2.475.214, Manaus, Brazil. Ten post-bariatric patients under outpatient follow-up were screened. All presented recurrent diarrhea for at least three months despite a minimum of three prior antibiotic treatments. Inclusion criteria included a positive breath test for SIBO, altered functional stool analysis, or confirmed Clostridioides difficile infection by fecal toxin assay. Potential donors, preferably first-degree relatives, underwent clinical assessment and laboratory screening. Clinical and laboratory data were collected from both donor and recipient, including 16S rRNA fecal microbiota sequencing (Bioma4me™), bioelectrical impedance analysis, and habitual dietary intake assessment. Recipient evaluations were performed at baseline (T0) and 90 days after FMT (T1). The primary outcome was sustained resolution of diarrhea for at least 90 days following the procedure. Results: Of the ten patients screened, one met all inclusion criteria and underwent FMT. The procedure consisted of a single administration of 150 mL of fecal suspension diluted in 0.9% saline, delivered enterally via a nasoenteric tube positioned endoscopically in the distal alimentary limb. The treated patient achieved complete remission of gastrointestinal symptoms, maintained for more than 90 days. Conclusions: This clinical experience supported the development of an institutional FMT protocol and suggests potential benefit of FMT in selected post-bariatric patients with refractory SIBO. Nevertheless, larger studies with longer follow-up are required to establish the safety, efficacy, and reproducibility of FMT in this specific clinical setting. This study was funded by the Amazonas Research Foundation (FAPEAM).This clinical experience supported the development of an institutional FMT protocol and suggests potential benefit of FMT in selected post-bariatric patients with refractory SIBO. Nevertheless, larger studies with longer follow-up are required to establish the safety, efficacy, and reproducibility of FMT in this specific clinical setting. This study was funded by the Amazonas Research Foundation (FAPEAM). Grafical Abstract