Perioperative faecal microbiome dynamics in patients undergoing rectal cancer surgery in the IMARI-trial.

BACKGROUND

The gut microbiome influences health by regulating metabolism, modulating the immune system, and protecting against pathogens. Surgical interventions, antibiotics, and dietary changes can disrupt this balance. In rectal cancer surgery, the perioperative microbiome's role in selective digestive decontamination and ileostomy formation remains underexplored. This manuscript aimed to investigate perioperative microbiome dynamics in patients undergoing rectal cancer surgery, focusing on the impact of selective digestive decontamination and ileostomy.

METHODS

This study was part of the IMARI-trial. Faecal samples were collected before surgery and faecal or ileostomy samples on postoperative day 4. Microbial composition and diversity were assessed using 16S ribosomal RNA sequencing; alpha and beta diversity analyses were stratified by time point, ileostomy status, and selective digestive decontamination administration.

RESULTS

Of the 246 enrolled in the IMARI-trial, 214 patients were analysed. Postoperative samples showed significantly lower alpha diversity than preoperative samples, indicating reduced microbial richness and evenness across groups. Beta diversity analyses revealed distinct clustering between pre- and postoperative samples, with surgery explaining the largest variance in microbial composition (R2 = 15.6%; P < 0.001). Ileostomy status (R2 = 9.6%; P < 0.001) and selective digestive decontamination administration (R2 = 3.1%; P = 0.002) also contributed significantly. Notable taxonomic shifts included increased postoperative abundances of Enterococcus and Klebsiella, alongside reduced Firmicutes genera, particularly in ileostomy samples.

CONCLUSION

Surgery and perioperative factors induce significant, early microbiome alterations, favouring facultative anaerobes over obligate anaerobes. Although selective digestive decontamination selectively modulates specific taxa, its overall impact on diversity appears less pronounced than surgery and ileostomy status. These findings underscore the need for studies linking perioperative microbiome trajectories to clinical endpoints and for evaluating microbiome-informed perioperative strategies, including antibiotic stewardship, diet, or microbial therapeutics, in rectal cancer care.

© The Author(s) 2026. Published by Oxford University Press on behalf of BJS Foundation Ltd.