Gut microbiota is a complex ecosystem of bacteria, viruses, archea, protozoa and yeasts in our intestine. It has several functions which maintain human body equilibrium. Microbial "dysbiosis" can be responsible for several gastrointestinal diseases. To build a narrative review we performed a Pubmed, Medline, Embase search for English language papers, reviews, meta-analyses, case series, and randomized controlled trials (RCTs) by keywords and their associations. Gut microbiota is altered in several gastrointestinal diseases with very different pathophysiology. They range from multifactorial diseases such as irritable bowel syndrome (IBS), nonalcoholic fatty liver disease (NAFLD) and gastric and colorectal cancers, immune-mediated such as celiac disease, inflammatory bowel diseases (IBD), and antibiotic-related such as clostridium difficile infection (CDI). Microbial dysbiosis remodulation by probiotics is feasible and safe in some of them. Gut microbial dysbiosis is statistically associated with several gastrointestinal diseases, affecting their pathophysiology. Its reverse by probiotics has some promising evidence of efficacy.