Genomic Characterization of Staphylococcus epidermidis and Staphylococcus hominis Isolated from Traditional Homemade Yogurt in Eastern Anatolia

Traditional fermented dairy products, such as homemade yogurt, host diverse microbial communities that may act as reservoirs for antibiotic resistance genes. This study aimed to genomically characterize Staphylococcus epidermidis and Staphylococcus hominis strains isolated from homemade yogurt to evaluate their ecological adaptability and potential public health risks linked to antimicrobial resistance. Yogurt samples were collected from the Berçelan Plateau of Hakkari, Türkiye. All isolates were identified as Gram-positive, catalase-positive, oxidase-negative cocci. Whole-genome sequencing showed that S. epidermidis carried a broader range of antibiotic resistance genes, active CRISPR/Cas systems, and fewer mobile genetic elements. In contrast, S. hominis had a smaller genome, more protein-coding genes, and a higher number of mobile genetic elements, but lacked CRISPR/Cas systems. These differences suggest divergent genomic strategies for adaptation and gene flow regulation. The detection of antimicrobial-resistant Staphylococcus strains in traditionally fermented yogurt highlights the importance of monitoring artisanal food products. Homemade dairy may serve as a niche for the persistence and potential spread of resistance genes, underlining the need for microbiological safety practices in non-industrial food systems.