Your immune system is the group of cells and molecules that protect you from disease by monitoring our body and responding to any foreign (non-self) substances they perceive as threats, particularly infectious microbes. Your immune system has co-evolved along with your microbiome, not only to create defenses against pathogens, but also to develop tolerance for beneficial microbes. There is a mutualistic relationship between your immune system and your gut microbiota, regulating one another and cooperating to support each other highlighted by the fact that 70–80% of your immune cells are found in your gut.

The dialogue between your immune system and your microbiome begins at birth. As you grow, the microbiome shapes the development of your immune system, and the immune system shapes the composition of the microbiota. This communication and mutual regulation is maintained throughout life creating the foundation for healthy interaction between the gut and the immune system.

In normal conditions, the immune system promotes the growth of beneficial microbes and helps maintain a stable microbial community, while in return, a healthy microbiome produces molecular signals that support the development of immune cells and contribute to the fine tuning of immune responses. A healthy crosstalk between the gut and the immune system supports protective responses against pathogens, promotes tolerance to harmless microbes and their products, and helps maintain self-tolerance (the ability of your immune system to not react harmfully to your own body).


The intestinal wall is the primary interface between the gut and your body. It ac