Spectrum-dependent dysbiosis and recovery patterns of the gut microbiota following antimicrobial exposure

Broad-spectrum antimicrobials profoundly alter gut microbial ecosystems; however, post-antimicrobial recovery remains incompletely understood. Here, we used a short-term oral exposure model in mice treated with clindamycin, moxifloxacin, or ceftriaxone, representing antimicrobials with distinct antibacterial spectra. Each antimicrobial induced distinct patterns of gut microbiota perturbation and cecal enlargement. At day 0, immediately after antimicrobial exposure, antimicrobial-specific differences in microbial composition and diversity were observed, followed by distinct recovery trajectories through days 3 and 5. Clindamycin induced sustained dysbiosis with limited recovery, whereas ceftriaxone caused pronounced initial disruption followed by partial recovery by day 5. Moxifloxacin produced transient perturbation with greater recovery of microbial diversity. Together, analyses of taxonomic composition, α-diversity, and β-diversity demonstrated that both the magnitude of the initial perturbation and early recovery were antimicrobial dependent. These findings delineate spectrum-dependent patterns of gut microbiota disruption and early recovery following antimicrobial exposure and highlight antimicrobial-specific effects on gut microbial resilience.