levels and risks for emergence of antimicrobial resistance, it is important to also consider the role of the enormously diverse human commensal microbiota. It is generally acknowledged that the use of antibiotics causes selection for and enrichment of antimicrobial resistance, but it has also been believed until recently that the commensal microbiota is normalized a few weeks following withdrawal of the treatment. As discussed above, increasing evidence suggests that this is not the case and that specific members of the microbiota may be positively or negatively affected for extended periods of time. With the onset of improved sequencing methods and other molecular approaches, increasing information is becoming available about how the biodiversity (richness and evenness) of the human microbiome is affected at different phylogenetic levels, from the community level to species, strains and individual clones. At the same time, it is possible to monitor the acquisition and persistence of resistance genes in the community. Together this information should help to provide knowledge of the natural dynamics of the normal microbiota and help us to understand the long-term consequences of antimicrobial treatment. This information is of great importance for the implementation of rational administration guidelines for antibiotic therapies.