Currently, studying the role of microbiome in the realization of antiviral mechanisms is a relevant issue, especially in the context of the COVID-19 pandemic. It is known that microbiome disrupts the life cycle of viruses in the human organism cells at different stages and stimulates both innate and specific immune response. Such factors as delivery by cesarean section, artificial feeding of a child, early use of antibacterial agents, age-related changes lead to the development of dysbiosis, which increases the body’s susceptibility to viral infections. A positive role of probiotics use is observed in a range of viral infections, including HIV, HPV infection, viral hepatitis, respiratory infections and a number of other diseases.