In recent years, there has been an exponential increase in interest to the human microbiome, a community of living microorganisms that colonize all external and internal surfaces of the body together with their microbial metabolites, organic compounds, and genetic material. Gut microbes are involved in a wide range of physiological functions, including the production of essential vitamins, bile salts, and short‑chain fatty acids such as butyrate; they inhibit tumor formation and inflammation, regulate glucose, lipid and energy exchanges; regulate adaptive immunity; play a central role in the development of immune tolerance to microbial and non‑microbial antigens and maintenance of the integrity of protective barriers. Resident microbes are important in the production of neurotransmitters including dopamine, serotonin and γ‑aminobutyric acid, as well as hormones such as glucagon‑like peptide 1 and a complex network of neurological, endocrine and microbial components involved in the homeostasis of the gut–microbiota–brain axis. Numerous studies have established the association between antimicrobial use, microbiome damage, and adverse health outcomes. Recently, by analogy with nephrotoxicity or hepatotoxicity, a new term «microbiotoxicity» has been proposed, which encompasses the unwanted side effects of antibiotics on the patient’s microbiome. It is emphasized that clinicians must carefully weigh the benefits of antibiotics in the treatment of infections against their microbiotoxic effects when making individual decisions about prescribing antibiotic therapy. An exception to this is rifaximin, with its atypical antimicrobial effects it is able to induce positive modulation of intestinal microflora, creating a favorable environment for the growth of bacteria useful for the host organism without changing their general composition. The review gives analysis of the role of the microbiome as a complex immunological, endocrine, and neurological ecosystem and the potentially harmful consequences of antibiotic exposure to it.
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