PREDIRES_phage
Background Antibiotics notoriously perturb the gut microbiota. We used untargeted and targeted phenotypic and genotypic approaches to study faecal samples collected up to 90 days following a 3-day course of intravenous ß-lactam antibiotics in 22 healthy volunteers. We studied the changes of the bacterial, phage and fungal components of the microbiota as well as the metabolome and the ß-lactamase activity of the stools. This allowed to assess their degrees of perturbation and resilience. Results  While only two subjects had detectable concentrations of antibiotics in their faeces, suggesting antibiotic degradation in the gut, the intravenous treatment perturbed very significantly the bacterial and phage microbiota, as well as the composition of the metabolome. In contrast, its impact was relatively low on the fungal microbiota. In the end of the surveillance period, we found evidence of resilience across the gut system since most components returned to a state similar to the initial one, even if the taxonomic composition of the bacterial microbiota changed. However, the dynamics of the different components overtime were rarely correlated. The richness of the resistome was significantly reduced up to day 30, while a significant increase in the relative abundance of ß-lactamase encoding genes was observed up to day 10, consistent with concomitant increase in the ß-lactamase activity of the microbiota. The level of ß-lactamase activity at baseline was associated with the resilience of the metabolome content of the stools.