Colorectal cancer (CRC) is one of the most prevalent malignant neoplasms that occupies the leading position in terms of cancer mortality. The main problem of CRC is that the disease is diagnosed at the advanced stages (about 50% of cases identified are stage III and IV CRC), which results in high mortality. Dysbiotic gut microbiota alterations represent one of the key risk factors of CRC. Three hypotheses of CRC emergence were formulated in order to explain the relationship between dysbiosis and carcinogenesis: “alpha-bug”, keystone pathogen, and driver–passenger hypotheses. The driver–passenger model is the most promising, it divides bacteria into “drivers” of cancer triggering inflammation and cell damage and the passenger bacteria modeling tumor microenvironment, accelerating tumor growth, and exacerbating dysbiosis. Drivers and passengers can be markers of various carcinogenesis stages. Colonoscopy involving examination of the surface of the rectum and colon is the most effective method to detect CRC, including the early stage disease. However, the wide use of this procedure is limited by the fact that it is associated with discomfort for patients and the risk of possible sequelae. Non-invasive microbiota assessment based on the driver–passenger model can become a safe and affordable alternative to the invasive diagnostics during preventive screening, since it makes it possible to improve survival rate due to involvement of a larger number of patients.