Antibiotic therapy can affect not only the target pathogen but also commensal inhabitants of the human host. The extent of the impact on non-target microbial populations depends on the particular antibiotic used, its mode of action and the degree of resistance in the community. Sometimes an imbalance in the commensal gut microbiota due to antibiotic administration can result in intestinal problems, such as antibiotic-associated diarrhoea (AAD) (McFarland, 1998). An additional concern is the increase in antibiotic resistance and the potential spread of resistance genes to pathogenic bacteria. Recently, it has been shown that even short-term antibiotic administration can lead to stabilization of resistant bacterial populations in the human intestine that persist for years. Although the consequences of long-term persistence of antibiotic resistance in the human gut are currently unknown, there are high risks that this could lead to increased prevalence of antibiotic resistance, reduce the possibility of successful future antibiotic treatments and subsequently lead to higher treatment costs. The short-term consequences of
antibiotic administration have previously been reviewed and have primarily dealt with culture-based analyses. This mini-review will focus on the long-term consequences of antibiotics on the composition, ecology and resistance of the human gut microbiota and will highlight some recent studies based on molecular methods.