Metagenomic Comparison of Gut Microbiota Structure and Function Between Wild and Domestic Cats

The domestication process has profoundly altered the dietary patterns and living conditions of cats with consequential effects on their gut microbiome. This study compared the gut microbiota composition and metabolic functions between wild and domestic cats using metagenomic sequencing. Taxonomic analysis revealed a significantly higher microbial diversity and distinct microbial community structure in wild cats compared to domestic cats. The gut microbiota of domestic cats was characterized by a significant enrichment of Bacteroidota and genera associated with carbohydrate metabolism, such as Segatella. In contrast, wild cats exhibited an enrichment of Bacillota, Actinomycetota, and protein-fermenting genera like Clostridium, alongside a higher carriage of potential pathogens. Functional analysis further revealed a systematic reprogramming of microbial metabolic strategies. The gut microbiome of domestic cats shifted toward efficient hydrolysis of dietary polysaccharides, enhanced endogenous biosynthesis, and internal metabolic homeostasis, aligning with a stable, processed diet. Conversely, the wild cat microbiome was optimized for the robust degradation of complex, irregular substrates from natural prey, exhibiting heightened activity in pathways supporting protein fermentation, alternative energy extraction and antioxidant defense. These findings indicate that felid domestication drives a fundamental transition in gut microbial function, closely linked to concomitant changes in diet and environmental exposure.