**Abstract**

The purpose of this chapter is to illustrate the role of the intestinal barrier in keeping separate, but also communicating, the "world above" represented by the resident microbial flora (microbiota) and the "world below" (the immune system associated with the gastrointestinal tract or GALT). Description will be given for how it is possible that the intestinal microbiota, in the course of *dysbiosis*, can alter the junctional complex that unites the enterocytes, and how the probiotic bacteria (and their metabolites) to restore a homeostasis in the gastrointestinal tract. The fundamental role of enterocyte mitochondria will be highlighted, where being archaic methylotrophic bacteria have retained the ability to "interpret" the bacterial signals (*eubiotic* or *dysbiotic*) derived from the intestinal lumen. In this perspective, everything starts from an altered mitochondrial functioning, deriving from a condition of *dysbiosis*, which alters the tightness of the TJs, opening up to bacterial translocation and bacterial products. Probiotics and their metabolites act by restoring mitochondrial activity and function and the enteric barrier functionality. The author will exemplify this "story" with *in vitro* and *in vivo* tests, deriving from original studies on different animal models (mouse, dog, and cat) including humans (patients with IBD and with HIV-related enteropathy).

**Keywords:** tight junctions, mitochondria, microbiota, Toll-like receptors, innate immunity, oral tolerance, probiotics
