Metagenomic profiling reveals autochthonous strains with starter culture potential and highlights safety considerations in artisanal ayran

Abstract

Industrial production of ayran could benefit from custom autochthonous starter cultures, as the organoleptic properties are strongly influenced by microbiota, producing enzymes, secondary metabolites, and exopolysaccharides (EPS). Here, we used shotgun metagenomic sequencing to characterise microbiome, functional potential, and safety profile of 11 artisanal ayran samples and identify candidates for starter culture development. The microbiome was dominated by Streptococcus thermophilus and Lactobacillus (L.) delbrueckii, exhibiting substantial strain-level diversity that shaped functional profile of ayran. Diverse eps gene clusters, carbohydrate biosynthesis pathways, and procoagulant proteases indicated considerable technological potential among indigenous strains, providing a source of potential starter culture candidates. However, safety assessment highlighted the need for careful evaluation of starter candidates, as some strains carried acquired antibiotic resistance genes (ARGs) linked to mobile genetic elements (MGEs) or virulence factors. These findings indicate that new starter cultures are needed to minimise potential health and safety concerns associated with artisanal ayran products.