In the intestine, the microbial genomes and repertoire of biochemical reactions outnumber those of the host and significantly contribute to many aspects of the host's health, including metabolism, immunity, development and behavior, while microbial community imbalance is associated with disease.

The crosstalk between the host and its microbiome occurs in part through the secretion of metabolites, which have a profound effect on host physiology. The immune system constantly scans the intestinal microenvironment for information regarding the metabolic state of the microbiota as well as the colonization status. Recent studies have uncovered a major role for microbial metabolites in the regulation of the immune system. In this review, we summarize the central findings of how microbiota-modulated metabolites control immune development and activity.