Inflammatory bowel disease (IBD) may develop due to an immunogenic response to commensal gut microbiota triggered by environmental factors in the genetically susceptible host. Isotretinoin, applied in the treatment of severe acne, has been variably associated with IBD, but prior treatment with antibiotics, also associated with IBD development, confounds confirmation of this association. This study investigated the effects of doxycycline, metronidazole (frequently used in the treatment of acne and IBD, respectively) and isotretinoin on murine gut (faecal) microbiota after 2 weeks of treatment and after a 4-week recovery period. Faecal microbiota composition was assessed by 16S rRNA gene sequencing on the GS-FLX 454 platform with primers directed against the variable regions V1-V2. Doxycycline had a modest effect on bacterial richness and evenness, but had pronounced persistent and significant effects on the abundance of certain operational taxonomic units compared with the control group. In contrast, metronidazole induced a pronounced reduction in diversity after treatment, but these effects did not persist after the recovery period. This study demonstrates differential effects of antibiotics on the gut microbiota with doxycycline, unlike metronidazole, mediating long-term changes in the murine gut microbiota. Isotretinoin had no significant effect on the faecal microbiota.