Dysregulation of the microbiome has been associated with development of complex diseases such as obesity and diabetes. However, no method has been developed to control disease-associated commensal microbes. We investigated whether immunization with microbial antigens, using CpG oligodeoxynucleotides (CpG-ODN) and/or curdlan as adjuvants, induces systemic antigen-specific immunoglobulin (Ig)A and IgG production and affects development of diseases in mice.