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

genomics
microbiology
molecular-biology

Abstract

Background: Traditional fermented dairy products, such as homemade yogurt, harbor complex microbial communities that may act as reservoirs for antibiotic resistance genes. Understanding the genomic characteristics of these microorganisms is crucial for evaluating their ecological adaptability and potential public health risks—including the dissemination of resistance determinants via horizontal gene transfer within artisanal food environments.

Methods: Staphylococcus epidermidis and Staphylococcus hominis isolates were obtained from homemade yogurt samples collected in the Berçelan Plateau of Hakkari, Türkiye. Phenotypic identification was performed through Gram staining and biochemical profiling (catalase and oxidase tests). Whole-genome sequencing and comparative genomic analyses were conducted to evaluate antibiotic resistance gene content, CRISPR/Cas systems, mobile genetic elements, and overall genomic structure.

Results :All isolates were identified as Gram-positive, catalase-positive, and oxidase-negative cocci. Genomic analysis revealed that S. epidermidis possessed a broader antibiotic resistance gene repertoire and an active CRISPR/Cas system, alongside fewer mobile genetic elements, indicative of increased genomic stability. Conversely, S. hominis exhibited a smaller genome size but a higher number of protein-coding sequences and mobile elements while lacking CRISPR/Cas systems. These differences suggest distinct evolutionary strategies for adaptation and genome maintenance in homemade yogurt environments.

Conclusion :The presence of antimicrobial-resistant Staphylococcus strains in traditionally fermented yogurt underscores the necessity of routine microbiological surveillance in non-industrial food production settings. The genomic features identified highlight the potential for artisanal dairy environments to support the persistence and spread of resistance genes. Strengthening safety measures in traditional fermentation practices is therefore essential to mitigate emerging risks associated with antimicrobial resistance.

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