Changes in the gut microbiome in colon cancer surgery patients: a pilot observational study

Between March and September, 2019 we included 27 adult patients who were scheduled to undergo elective colorectal cancer surgery. We performed a prospective descriptive observational study whose primary aim was to evaluate changes in the gut microbiome before and after surgery, and to evaluate the effect of different prophylaxis regimens (standard prophylaxis with cefuroxime and metronidazole versus carbapenems for ESBL-E carriers). We obtained rectal sample before and 3 days after surgery, and an intraoperative intraluminal stool sample. We performed metataxonomics analysis based on sequencing of the bacterial 16S rRNA gene marker.We observed large and significant increases in the genus Enterococcus between both the preoperative and intraoperative samples and the post-operative sample, mainly driven by Enterococcus faecalis. There were significant differences in the postoperative microbiome between patients who received standard prophylaxis and carbapenems, specifically in the family Erysipelotrichaceae. Preoperative haemoglobin and prealbumin levels were associated to post-operative differences in gut microbiome.