The impact of surgery on the intestinal microbiome is hypothesed to be due to phenotypic shifts in pathogenic bacteria as a result of the surgical injury.
An association has been described between a specific commensal bacteria (Enterococcus Faecalis) and activation of MMP-9, that may have a role in increased risk of anastomotic leak.
Oral antibiotics, probiotics and avoidance of intestinal ischemia may all have a role in reducing colonisation of these bacteria around the newly formed anastomosis.
Related paper: Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak