Functional Profiling of Antimicrobial Resistance in Rabbit Gut Microbiome

Abstract

Antimicrobial resistance (AMR) is a growing concern in laboratory animals, where antibiotic use can disrupt the gut microbiome and promote resistant strains. Rabbits, commonly used in biomedical research, are particularly susceptible to gut dysbiosis, increasing the risk of infection and subsequent antibiotic use. This study used 16S rRNA amplicon sequencing and PICRUSt2 to predict resistance-related functions in rabbits under standard laboratory conditions. Among 2427 amplicon sequence variants, 42 functional classes were identified, with AMR comprising 1.55% of the predicted functions, including beta-lactam, vancomycin, and cationic antimicrobial peptide resistance. These AMR functions were associated with commensal genera such as Bacteroides and Ruminococcus, while no associations were observed with pathogens such as Escherichia or Salmonella. The study provides functional evidence of intrinsic AMR in the rabbit gut microbiome and underscores the importance of antimicrobial stewardship in laboratory animal research.