Obesity and diabetes, both rapidly increasing in prevalence worldwide, have a tremendous medical and socio-economic impact. Both are multifactorial in their etiology, influenced by genetic and environmental factors. Obesity and Diabetes also share the characteristic of a chronic low-grade inflammatory state, that indicates that altered metabolism may alter the immune system. The gut microbiota, and microbial metabolites in particular, have been described to play an important role in disease development. However, the underlying mechanisms are still ill-defined.