Abstract
Surgical interventions involving the gastrointestinal tract profoundly influence the composition, diversity, and function of the gut microbiota, which plays a central role in human health and disease. Recent advances in sequencing technologies, particularly 16S rRNA gene profiling and metagenomics, have enabled detailed characterization of microbial alterations following different types of intestinal surgery. Bariatric procedures such as Roux-en-Y gastric bypass and sleeve gastrectomy consistently reduce microbial diversity in the short term but are also associated with functional reprogramming of the microbiota, including enhanced capacity for energy harvest and altered bile acid metabolism. Gastrectomy and bowel resections induce region-specific changes, often leading to dysbiosis, small intestinal bacterial overgrowth, and nutrient malabsorption. The creation of intestinal stomas modifies luminal and mucosal microbial communities, frequently promoting the overrepresentation of opportunistic pathogens. In addition, perioperative interventions, including mechanical bowel preparation, perioperative fasting, and antibiotic prophylaxis, exert acute but sometimes long-lasting effects on microbial ecology. These microbial shifts have been linked to a broad spectrum of clinical outcomes ranging from metabolic improvements and enhanced immune modulation to increased susceptibility to infections, impaired wound healing, and long-term complications such as anastomotic leaks or inflammatory conditions. Understanding the relationship between specific surgical procedures, perioperative management, and microbiota modulation is therefore crucial for optimizing patient outcomes. This review integrates current evidence from clinical and translational studies, highlights the mechanistic links between surgical approaches and microbial dynamics, and outlines future directions for research and therapeutic interventions aimed at preserving or restoring a healthy microbiome after intestinal surgery.