Antibiotics can treat serious infections but may come with side effects. Veterinarians may prescribe antibiotics to cats to treat or prevent infections caused by harmful bacteria. However, since antibiotics cannot distinguish between 'bad' and 'good' bacteria, they eliminate all bacteria, disrupting the diversity and balance of the microbiome. Restoring a diverse microbiome takes considerable time, during which infectious bacteria may thrive in the gut. Antibiotics should be used only when necessary and according to guidelines. 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 antibiotics include amoxicillin, cephalexin, doxycycline, clindamycin, gentamicin, enrofloxacin, and penicillin. Cats with imbalanced gut microbiomes should be treated with antibiotics more cautiously to facilitate healthy recovery.