In the past decades the view of the gut microbiota has transformed from fighting the bad bugs with antibiotics to protecting the good bugs that function as a defense barrier and contribute to overall health. The gut microbiota is now commonly recognized as a separate “organ” that, together with the human genome and the immune system, constitutes 1 of the 3 pillars that support human health. The complexity of interactions of the microbiota with not only the host genome and the immune system, but also with the endocrine system, brain, and nutrition, makes it a challenge to grasp the overall picture regarding the role of the microbiota in human health.