Antibiotics can treat dangerous infections, but they may come with side effects. Veterinarians may prescribe antibiotics to dogs to treat or prevent infections caused by harmful bacteria. However, antibiotics cannot distinguish between 'bad' and 'good' bacteria, so they eliminate all bacteria, disrupting the diversity and balance of the microbiome. Restoring a depleted microbiome can take significant time, and it can create an environment favorable for the proliferation of infectious bacteria. Antibiotics should be used only when necessary and following guidelines for appropriate use. Misuse of antibiotics can lead to the formation of antibiotic-resistant bacteria, making it difficult to suppress harmful bacteria even with antibiotic treatment.

Antibiotics are commonly used for urinary tract infections, ear infections, respiratory infections, skin infections, and eye infections. Some common antibiotics include amoxicillin, cephalexin, doxycycline, clindamycin, gentamicin, enrofloxacin, and penicillin. Dogs with imbalanced gut microbiomes should be treated with antibiotics more cautiously to aid in a healthy recovery.