A variety of antibiotics have been developed and their activities improved since the discovery of penicillin by Alexander Fleming. At present, antibiotic drugs are the most important drugs for the treatment of many infectious diseases caused by pathogenic bacteria fulfilling Koch’s postulates. Current major challenges in medicine are to establish preventive and treatment strategies for chronic inflammatory diseases such as allergic disease, inflammatory bowel disease, autoimmune disease, and non-communicable diseases including cancer, cardiovascular disease, chronic respiratory diseases, diabetes. Recent advances in gut microbiota research have led to numerous discoveries showing that gut commensal bacteria play essential roles in the development and regulation of the host immune system. There is accumulating evidence that the imbalance of compositions or functions of gut microbiota (termed as dysbiosis) is associated with the pathogenesis of chronic inflammatory diseases. This review summarizes the pros and cons of antibiotic treatments altering gut microbiota in dysbiosis-associated diseases.

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Recently, fecal microbiota transplantation (FMT), a therapeutic approach used to restore normal intestinal microbiota functions by transplanting bacterial microbiota from feces derived from a healthy donor, has been evaluated in the context of treating patients. The therapeutic potential of FMT in treating various diseases has been extensively investigated in recent years. The high efficacy of FMT in therapy for refractory Clostridium difficile infection (rCDI), an intestinal disease also linked to dysbiosis, was demonstrated by van Nood et al. However, the efficacy of FMT treatment in patients with ulcerative colitis (UC) remains controversial. In 2017, a third randomized controlled trial was reported in Australia. A multidonor intensive FMT was practiced five times a week for eight weeks resulting in remission and positive responses. This multidonor intensive FMT proved its efficacy, however FMT is time intensive, and complications are a possibility. We previously reported that FMT following multiple antibiotic therapy (AFM: amoxicillin, fosfomycin and metronidazole) synergistically contributed to the recovery of the phylum Bacteroidetes composition, which is associated with the endoscopic severity of UC and a high clinical improvement rate. We named this combination therapy with FMT, A-FMT (Antibiotics plus FMT, and AFM plus FMT). A-FMT alleviated intestinal dysbiosis, including loss of species diversity among Bacteroidetes in patients with UC. Eradication of dysbiotic indigenous Bacteroidetes species by AFM pretreatment may promote the entry of living Bacteroidetes cells, thereby improving the dysbiosis of intestinal microbiota induced by UC. Currently, no standard practice for administering FMT therapy has been established. This highlights the need for the development of more effective, simple, and personalized strategies for performing FMT, for different types of disease.

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