Integrated Metagenomic and Untargeted Metabolomic Analyses Characterize Enramycin-Associated Colonic Microbial and Metabolic Changes in Weaned Rabbits

Abstract

Simple Summary Digestive disorders are common after weaning and can compromise rabbit health. Enramycin is a dietary antimicrobial used in young animals, but its broader effects on the intestinal ecosystem remain unclear. This study evaluated the short-term effects of dietary enramycin supplementation in weaned rabbits by combining clinical observations with colonic microbiota and metabolite analyses. During the 14-day trial, enramycin significantly reduced diarrhea incidence but did not improve body-weight development or major organ indices. Supplementation was accompanied by alterations in selected microbial groups, metabolic features, and antibiotic resistance-related characteristics. However, because these ecological analyses were conducted in a limited subset of surviving rabbits without recorded diarrhea, these changes should not be interpreted as the direct mechanism underlying the reduced diarrhea incidence. Nevertheless, the findings indicate that enramycin may provide short-term benefits for diarrhea control while simultaneously influencing the intestinal ecological environment. Therefore, enramycin dosage and duration should be carefully considered in weaned rabbits. The results highlight the importance of weighing potential short-term benefits against broader ecological effects when evaluating dietary antimicrobial use.