Microbiota of the digestive system consists of many different types of bacteria but also viruses, fungi, archaea, and protozoans. In healthy adults, the gut microbiota is primarily composed of six phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria and Verrucomicrobia are the most common phyla of microorganisms in the intestinal tract of humans and play a key role in the nutrient absorption, and support the strengthening of the intestinal barrier. The microbiome is of great importance for the development of the immune system and homeostasis. Dysbiosis, or changed composition of healthy microbiota, is associated with the pathogenesis of diabetes and is a possible risk factor in its development. Diabetes mellitus is a persistent metabolic condition characterized by high blood sugar levels, resulting from either insufficient production of insulin or the body's resistance to insulin. Along with animal studies, numerous studies on humans have reported increased or decreased numbers of specific gut bacteria and their metabolites in diabetics compared to healthy controls. Basic mechanisms linking specific gut microbiota to metabolic diseases include increased energy absorption from food, changes in host genetic expression, regulation of energy consumption and storage, and changes in gut permeability. This can result in metabolic endotoxemia, inflammation and the development of insulin resistance. Manipulation of microbiota with probiotics, prebiotics, diet and transplantation of fecal microbiota can modulate early interactions between the host and microbiota by enabling beneficial microorganisms with protective potential and thus be used in treatment for diabetes.