Microbial Community Structure and Functional Profiles of Traditional Kazakh Suzbe Across Geographically Distinct Regions

Traditional Suzbe is a fermented dairy product widely prepared at the household level in Kazakhstan, but the composition and functional potential of its microbiota remain poorly characterized. In this study, shotgun metagenomic sequencing was used to investigate the microbial communities of 20 traditional Suzbe samples collected from five geographically distinct regions of Kazakhstan. Lactic acid bacteria dominated the microbial communities, with annotations assigned to Lactococcus lactis, Lactococcus cremoris, and Streptococcus thermophilus present in all samples. Alpha diversity did not differ significantly among the five regions, and PERMANOVA did not detect statistically significant regional differences in overall microbial community composition (R2 = 0.253, p = 0.216). Nevertheless, LEfSe analysis identified several region-associated taxa, mainly among less abundant members of the microbiota. Functional annotation using the KEGG database showed that carbohydrate metabolism, amino acid metabolism, energy metabolism, cofactor and vitamin metabolism, and membrane transport were among the major functional categories. Functional PERMANOVA did not detect statistically significant regional differences in overall functional composition (R2 = 0.249, p = 0.276), although several metabolic pathways differed in relative abundance. Overall, the sampled Suzbe microbiomes were dominated by lactic acid bacteria, with several species detected in all samples and major functional categories detected across regions. Region-associated differences were identified among specific taxa and metabolic pathways; the nonsignificant PERMANOVA results do not establish taxonomic or functional conservation. This study provides new metagenomic data on traditional Suzbe and contributes to a better understanding of fermented dairy microbiota in Central Asia.