The Microleaks study: 16S community profile and metagenomic shotgun sequencing signatures associated with anastomotic leak

Anastomotic leaks (AL) are the most severe complications of colorectal surgery. The cause of AL is unclear, but recent studies have implicated the intestinal microbiota in its development. We aimed to determine whether there is an identifiable microbial pattern in the mucosal microbiota associated with AL. A pragmatic series of 162 patients undergoing colorectal resection with anastomosis had swabs taken from the proximal and distal mucosa of the bowel resection immediately after the tissue was excised. DNA was extracted for 16S rRNA amplicon gene sequencing and a subset for metagenomic shotgun sequencing (MGS). The AL rate in the cohort was approximately 15% (25/162). The alpha diversity measures from the intraoperative swabs were all significantly increased for AL, and there were significant differences in the beta diversity measures for AL from both the 16S and MGS datasets. The predictive power of AL was more sensitive when both proximal and distal communities were considered, and the species-level classifier AUC-ROC was stronger for the MGS dataset than for the 16S data (AUC = 0.92 and 0.76, respectively). We also report, for the first time, the functional changes in intraoperative AL microbes and noted an increase in the relative abundance of pathways with fermentation end products. This result was also found in our murine model of anastomoses (n = 20). At the time of surgery, the mucosal microbiota of the anastomotic extremities exhibits subtle differences at the species level and altered fermentation capacity, which may be associated with AL outcomes. A greater understanding of these insights could improve AL prognosis and preoperative management to reduce the occurrence of this life-threatening condition.