The gastrointestinal microbiome plays an important role in metabolism and vital physiological processes within the host, protects the organism from pathogens, affects the immune system and overall health of the host. Most bacteria within the microbiome can be classified into 5 groups: Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria. Various factors, such as age, environment, diet, maternal microbiome and various others can influence the composition of the microbiome community. Changes in the composition and diversity of the intestinal microbiome are associated with various gastrointestinal and systemic diseases. Also, various diets can lead to changes in the microbiome's composition and consequently to changes in metabolite production. The intestinal microbiome in healthy dogs and cats is resistant, adaptable and able to return to it’s basic composition after the animal returns to it’s usual diet. That shows us that a permanent change in the composition of the microbiome requires a long-term application of a specific diet. Therapeutic methods for treating dysbiosis include prebiotics, probiotics, antibiotics, and fecal microbiome transplantation. When probiotics pass through the GI tract, they produce metabolites that can alleviate clinical signs and modify the composition of the microbial community. FMT is a very interesting method of therapeutic treatment that could be a great tool to help with dysbiosis recovery in the future. However, further studies are needed to change it’s potential and limitations. Future research in the field of the intestinal microbiome should be aimed at elucidating the mechanisms of interaction between the microbiome and the host, the influence of the microbiome on the pathogenesis of various diseases and evaluating the effectiveness and sustainability of various therapeutic treatment methods used in intestinal dysbiosis.