The present invention relates to a method for predicting the incidence of a colon tumor, such as a colon polyp and colon cancer, and a causative factor thereof through metagenomic analysis of a bacterium-derived vesicle present in a human body-derived substance. More particularly, the present invention relates to a method for diagnosing a causative factor of a colon tumor and the risk of the incidence thereof by sequencing a metagenome present in a bacterium-derived vesicle present in excrement or urine. There are trillions of bacteria in an intestine, and the bacteria secrete vesicles out ofthe cells thereof for the purpose of information exchange. The bacteria are not absorbed into epithelial cells in a colon, but the vesicles secreted therefrom pass through the mucous membrane, are absorbed into the colonic epithelial cells, are distributed throughout the body via blood, and then are excreted through a liver and a kidney. The bacteria-derived vesicles may increase or decrease the occurrence of inflammation and cancer, and the present invention can be useful as a method for diagnosing the risk of the incidence of a colon tumor or a causative factor thereof by sequencing a genetic metagenome of a bacterium-derived vesicle present in a human body-derived substance. Further, an early diagnosis can still be made even after the incidence of a colon polyp or the onset of colon cancer, and the incidence of colon cancer can be lowered, and the treatment effect can be enhanced.