Urban stray cats are in close contact with humans and are important potential vectors for zoonotic diseases. However, comparative studies in the gut microbiota of cats living in different environments remain limited. Here, we conducted a comparative analysis of the gut microbiota between stray and domestic cats using 16S rRNA gene sequencing of fecal samples from 14 stray and 11 domestic cats in Hefei, China. Domestic cats harbored significantly higher alpha diversity (Sobs index, Padj. = 0.039; Shannon index, Padj. = 0.024) and more complex microbial co-occurrence networks than stray cats. Beta diversity analysis confirmed distinct community structures between the groups. Linear discriminant analysis identified 12 taxa enriched in stray cats, including Escherichia-Shigella and other potential opportunistic pathogens. Functional prediction indicated that the gut microbiota of domestic cats was enriched in genes related to DNA repair and cellular structure maintenance, whereas that of stray cats showed higher abundance of functions associated with secondary metabolism, defense mechanisms, and stress response. Phenotypic prediction further revealed increased proportions of stress-tolerant and facultatively anaerobic bacteria in stray cats. These findings demonstrate that lifestyle and environmental exposure shape the feline gut microbiota, with stray cats exhibiting a less diverse, more stress-adapted, and potentially pathogen-enriched microbial profile. This study provides insights into the ecological adaptation of gut microbiota and highlights implications for zoonotic risk and One-Health-oriented management of urban cat populations.
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