The intestinal microbiome has become a topic of intense scientific research, especially in the last 20 years, due to the hypothesis that it could have a critical influence in health and disease. Dysbiosis was the term coined to define the imbalance in intestinal microorganisms' equilibrium. More recently, a new wave of progress is taking place in this field, due to the emergence of high throughput technologies and big data analyses (Tropini, Earle, Huang, & Sonnenburg, 2017). In this mini review, we highlight the central concepts that we believe crucial to understand microbial behavior in the gut, in the brain, and its interaction with the immune system with a focus on antimicrobial peptides (AMPs). A great part of our point of view rely on experiments performed not only by our research group, but also by prominent scientists in the field during the last decade. Finally, we provide some provocative ideas to serve as a bridge and to provide linearity to such a fragmented area. Variation in microbial localization and density has been described along the entire intestinal tract with important pathophysiological implications (Tropini et al., 2017). Indeed, a tight balance is necessary to maintain homeostasis and when deregulated, the microbiota can promote not only intestinal diseases, but also affect distant organs. Among them, much attention has been directed to the brain, since brain and gut communicate through a number of complex pathways that include the central and autonomic nervous system, the hypothalamus-pituitary axis, and the enteric nervous plexuses (Mukhtar, Nawaz, & Abid, 2019). The gut-brain axis interacts in a bidirectional manner. Intestinal diseases can influence the brain and vice versa. In some cases, individual taxa are associated with a disease, whereas in other diseases,