Provided are vesicles derived from bacteria belonging to the genus Cupriavidus, a composition and a use thereof, wherein the vesicles or composition may be usefully used for the purpose of developing a method of diagnosing a malignant diseases such as gastric cancer, colon cancer, pancreatic cancer, cholangiocarcinoma, breast cancer, ovarian cancer, bladder cancer, prostate cancer, head and neck cancer, lymphoma, and the like, heart diseases such as cardiomyopathy, atrial fibrillation, variant angina, and the like, chronic obstructive pulmonary disease, stroke, diabetes, kidney failure, dementia, Parkinson's disease, or depression.