Antibiotic Course Frequency and Recovery Strategies Alter Gut Microbial Composition and Metabolism

Antibiotics profoundly alter the gut microbiome, but how different exposure frequencies shape microbial recovery and function remains unclear. The effectiveness of post antibiotic interventions such as probiotics or autologous fecal microbiota transplantation (aFMT) also requires further exploration. This study investigated how antibiotic course timing and recovery strategies influence gut microbial composition and metabolism in male Wistar rats. A single oral dose of vancomycin-ciprofloxacin (VC) caused rapid metabolic shifts in urine and feces within 8-12 hours and reduced bacterial α-diversity in cecal and colonic contents. When three VC courses were administered at regular (every 3 weeks; VCr) or irregular (1–3 weeks; VCi) intervals, VCr showed greater suppression of fecal α-diversity and stronger disruption of amino acid and host-microbial co-metabolism than VCi. Across the subsequent 3-week recovery period, VCr exhibited slower restoration of fecal α-diversity. At recovery week 3, β-diversity remained significantly different between VCr and VCi, and VCr showed persistently reduced cecal butyrate levels. Both groups showed elevated levels of 5-aminovalerate in feces and colon compared with untreated controls, whereas only VCi showed reductions in jejunal and ileal amino acids. Probiotics or aFMT had limited influence on these small intestinal alterations. However, aFMT accelerated recovery of fecal α-diversity, and both interventions promoted partial normalization of fecal amino acids and 5-aminovalerate, without achieving complete metabolic restoration. Overall, shorter intervals between antibiotic courses exerted stronger effects on the small intestinal luminal chemical environment, whereas longer recovery windows led to more pronounced suppression of colonic and fecal microbial metabolism. Probiotics and aFMT supported selective aspects of metabolic recovery but did not fully reverse antibiotics-induced disturbances, highlighting the need for more targeted post-antibiotic restoration strategies across different regions of the gastrointestinal tract.