Fecal microbiota transplantation and peri-stoma microbiome management in patients with intestinal stomas: from mechanisms to clinical translation

Background Fecal diversion-induced dysbiosis in the defunctioned intestinal segment represents a common pathogenic basis for diversion colitis, anastomotic leakage, and long-term metabolic sequelae in patients with permanent stomas. This review proposes the novel concept of “Peri-stoma Microbiome Management (PSMM)” and critically evaluates the clinical evidence for fecal microbiota transplantation (FMT), defined microbial consortia, bacteriophages, and postbiotics. It is important to emphasize that PSMM is a proposed conceptual framework; most of its components have not been prospectively validated in stoma patients. Main body The core pathological process involves a dramatic reduction in butyrate-producing obligate anaerobes, depriving colonocytes of their primary energy substrate. In experimental models, butyrate depletion impairs mitochondrial function and autophagic flux, with subsequent NLRP3 inflammasome activation; whether this pathway operates identically in the defunctioned human colon remains to be directly investigated. Collagenolytic pathobionts such as Enterococcus faecalis may expand under antibiotic pressure and secrete matrix metalloproteinase-9 that degrades anastomotic extracellular matrix. However, anastomotic leakage is a multifactorial complication, involving tissue ischemia, tension, patient comorbidities, and microbial factors. The PSMM framework encompasses four phases: (I) pre-stoma creation microbial pre-habilitation and risk prediction; (II) microbiota monitoring and intervention during stoma maintenance; (III) pre-reversal targeted decolonization using bacteriophages and engineered microbiota reconstruction; and (IV) long-term metabolic maintenance for permanent stoma carriers. Bacteriophages show promise for precision decolonization but face significant challenges, including bacterial resistance, narrow host range, manufacturing complexity, and regulatory barriers. Multi-omics monitoring remains aspirational due to high costs, long turnaround times, and lack of clinical integration. Conclusion The PSMM framework provides a structured conceptual approach for integrating microbiome-targeted strategies into the care of patients with intestinal stomas. However, most interventions remain investigational and require validation in adequately powered randomized trials.