During the first years following intestinal resection, spontaneous physiological adaptations occur in patients with short bowel syndrome (SBS), allowing improvement of the absorptive capacity of the remaining intestine. This adaptation is particularly effective in SBS patients with the colon in continuity. The specific relationship between this intestinal adaptation and changes in the gut microbiota has not been studied in these patients. We hypothesize that there is a specific relationship between the microbiota and its metabolites and intestinal adaptive capacity, and that certain gut bacteria may promote this spontaneous adaptation.