Felis catus Raw sequence reads
As globally prevalent companion animals, domestic cat (Felis catus) relies on their gut microbiome for essential physiological functions including nutrient metabolism, immune regulation, and pathogen resistance. Despite this ecological importance, systematic characterization of feline gut microbial ecosystems remains limited.Results: Through deep metagenomic sequencing of 412 fecal samples representing diverse breeds, geographies, and dietary regimes, we generated 2,852 strain-resolved metagenome-assembled genomes (MAGs) spanning 514 species-level clusters, including 106 novel taxa. This expanded genomic catalog enabled identification of 24 persistent core microbiota and 132 putative probiotic candidates across the feline population. Enterotype stratification revealed two dominant ecological configurations: ET-P (Prevotella-dominant) and ET-CB (Collinsella-Blautia-Bifidobacterium consortium). Complementing these genomic insights, culturomics profiling of 2,904 bacterial isolates through full-length 16S rRNA sequencing resolved 35 known species, 75 putative novel species, and one novel genus (Clostridiaceae gen. nov.). Subsequent in vitro experiments, six candidate probiotic strains were selected, with five demonstrating significant probiotic properties by in vitro experiment. The efficacy of a combination of these five strains was evaluated in a domestic cat diarrhea model induced by pathogenic E. coli, it showed significantly better performance than antibiotics and commercial probiotic in reducing cytokine levels and alleviating diarrhea symptoms.Conclusion: This work provides a large-scale genomic resource for the feline gut microbiome, establishing the first dedicated repository (FelMGDB, https://FelMGDB.bacbase.com) for feline microbial genomics research. Our findings yield novel insights into feline gut microbial ecology, demonstrating the therapeutic potential of a defined probiotic consortium to enhance gastrointestinal health and mitigate enteric disorders. These advances establish a frame