Colorectal cancer is a very common malignancy with high mortality. Many factors influencing both the development and subsequent treatment, such as age, gender or genetic predisposition, are not modifiable. Others, such as stress, diet, physical activity or smoking, may be prevented by each individual. The gut microbiota is an important factor involved in both the development and treatment outcomes. With the advancing study of the gut microbiota, the relationship between its composition and various diseases is better understood. The proportions of members of the phyla Firmicutes (as beneficial microbiota) and Bacteroidetes (as mostly disease-associated microbiota) seem to be particularly important. Some studies suggest that certain bacteria may contribute to postoperative anastomotic leaks that prolong hospital stays, are a burden to patients, increase costs and may be fatal. Bacteria associated with the complication are, for example, enterococci, pseudomonads or bifidobacteria. Better understanding of the pathognomonic relationship between increased detection of certain bacteria and a complication may lead to individualized therapy aimed to reduce complications during surgical management of colorectal cancer.