The invention provides methods of treating disease, such as hypercholesterolemia (e.g., by modulating serum lipids, such as cholesterol, low-density lipoproteins, high-density lipoproteins, and triglycerides) and hyperglycemia by administering Bacillus Calmette-Guerin (BCG). Methods of the invention also encompass the use of genomic, proteomic, and metabolomic analyses for determining the likelihood that a patient has disease or will respond to treatment (e.g., with BCG therapy), as well as for determining whether a patient previously administered BCG would benefit from BCG redosing.