We recently found that the gut microbiota was dramatically perturbed after taking a treatment regimen commonly used for Helicobacter pylori infections, consisting of clarithromycin, metronidazole and omeprazole. Using 454 pyrosequencing we found that some members of the faecal microbiota were affected for extremely long periods of time, i.e. up to 4 years post-treatment. In addition, we also looked at the impact of antibiotic administration on the throat microbiota and found that the throat bacterial community was more resilient than the faecal bacterial community. The actinobacteria were particularly negatively impacted in both the throat and gut samples immediately after antibiotic treatment, presumably due to clarithromycin that is known to target this group. Adamsson et al. also previously found that this antibiotic treatment regimen led to quantitative and qualitative alterations in the faecal microbiota and suggested that amoxicillin might be better from an ecological perspective than clarithromycin for eradication of H. pylori because it resulted in less emergence of resistant strains.