Effects of oral antibiotics and isotretinoin on the murine gut microbiota

•Medications may modulate the gut microbiota favouring later development of inflammatory bowel disease (IBD).•IBD is associated with prior antibiotic use. An impact of isotretinoin is uncertain.•Isotretinoin had no significant impact on community composition or diversity.•Metronidazole induced a significant decrease in diversity that recovered within 4 weeks.•Doxycycline had modest direct effects but a lasting impact on composition at operational taxonomic unit level.