16S rRNA gene-based gut microbiota profiling of dogs and cats before and after probiotic administration

This study examined gut microbiota changes in dogs and cats following oral administration of Bifidobacterium longum CKD1, a probiotic candidate strain. Fecal samples were collected before and after 12 weeks of supplementation, and bacterial community profiles were analyzed by 16S rRNA gene (V3–V4 region) amplicon sequencing on the Illumina MiSeq platform. Sequence data were processed to identify Amplicon Sequence Variants (ASVs) and taxonomically annotated using the NCBI 16S reference database. This dataset provides a comprehensive overview of probiotic-associated microbial shifts in companion animals and offers a valuable resource for comparative studies on host-specific microbiota modulation and probiotic efficacy.