Outer membrane vesicles (OMVs) are spherical nanoparticles secreted by gram-negative bacteria, which are composed of outer membrane and bacterial components. These nanoparticles are secreted by bacteria under external pressure conditions, such as antibiotics, anaerobic and other adverse environments. These nanoparticles have special physiological activities in vivo. Some gram-negative bacteria secrete OMVs even during normal life cycle. OMVs play an important role in many physiological processes, such as response to stress, toxin transfer, pathogenicity, intercellular communication, immune regulation, gene transfer and maintenance of microbiota homeostasis, etc. When we use antibiotics, the microbiota is passively exposed to low doses of antibiotics, which results in the secretion of a large amount of OMVs. The release of OMVs will damage the intestine and induce various inflammations. The present paper reviewed the structure, production and physiological functions of OMVs and suggested that antibiotic exposure not only destroyed the normal flora but also led to the production of OMVs to induce chronic inflammations. Phage therapy does not destroy the normal flora, nor does it cause OMV releasing when killing the target bacteria. Therefore, the development of phage therapy targeting host bacteria will greatly reduce the side effects in treating infectious diseases.