Gut microbiome disruption in free-roaming cats: Do antibiotics reduce or restructure zoonotic risk?

Free-roaming cats are abundant in many urban ecosystems but pose significant public health and ecological risks as potential reservoirs of potential zoonotic pathogens. This study examined the gut microbiome of free-roaming cats in urban green spaces in Beijing, China, focusing on microbial diversity and potential zoonotic pathogen prevalence. Using 16S rRNA amplicon sequencing and the MBPD zoonotic pathogen detection pipeline, we identified multiple opportunistic zoonotic bacterial pathogens, including Clostridium perfringens, Pseudomonas stutzeri, Enterobacter cloacae, Aeromonas veronii, Klebsiella pneumoniae, Escherichia coli, Stenotrophomonas maltophilia, and Streptococcus salivarius (including ESKAPE pathogens). Antibiotic treatment was associated with reduced microbial diversity (Shannon index: 4.1–5.5 in non-treated cats vs. 1.9–4.7 in treated cats) and a lower relative abundance of key pathogens, including E. cloacae and K. pneumoniae. However, we observed a paradoxical shift in microbiome structure: in non-treated cats, higher microbial diversity was associated with lower pathogen abundance, whereas in treated cats, diversity positively correlated with pathogen presence, possibly due to microbiome instability or opportunistic recolonisation after antibiotic disruption. These findings highlight the complex trade-offs of antibiotic-driven microbiome disruption and highlight the need for microbiome-informed One Health interventions. Given the role of microbial diversity in pathogen suppression, alternative strategies—such as probiotic supplementation—may offer a more sustainable approach to mitigating zoonotic disease transmission while balancing urban biodiversity conservation and public health safety.