The excessively widespread use of antibiotics has created many threats. A well-known problem is the increasing bacterial resistance to antibiotics, which has clearly become a worldwide challenge to the effective control of infections by many pathogens. But, beyond affecting the pathogenic agents for which it is intended, antibiotic treatment also affects the mutualistic communities of microbes that inhabit the human body. As they inhibit susceptible organisms and select for resistant ones, antibiotics can have strong immediate effects on the composition of these communities, such as the proliferation of resistant opportunists that can cause accute disease. Furthermore, antibiotic-induced microbiota alterations are also likely to have more insidious effects on long-term health. In the case of the gut microbiota, this community interacts with many crucial aspects of human biology, including the regulation of immune and metabolic homeostasis, in the gut and beyond. It follows that antibiotic treatments bear the risk of altering these basic equilibria. Here, we review the growing literature on the effects of antibiotic use on gut microbiota composition and function, and their consequences for immunity, metabolism, and health.
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