Impact of Manufacturing Stages and Processing Scales on the Microbial Profile of Hurood

Traditional cheese products harbor complex microbial communities that influence their quality and safety. However, the effects of processing scale and manufacturing stage on the microbial profile of hurood, a traditional Mongolian cheese, remain poorly understood. This study examined microbial indicators, community composition, and succession dynamics across four manufacturing stages (raw milk, yogurt, whey, and hurood) and three processing scales (pastoral household, workshop, and factory) using plate counting and 16S rRNA gene amplicon sequencing. Twenty-four samples were collected from Xilin Gol, Inner Mongolia. Total aerobic plate counts and coliform counts decreased significantly from raw milk (7.30 and 4.49 log CFU/g, respectively) to hurood (2.02 and 0.34 log CFU/g, respectively; p < 0.05), reflecting progressive microbial reduction through acidification and thermal treatment, whereas yeast counts remained stable across stages. Firmicutes dominated the fermented stages, with Lactococcus and Lactobacillus as the predominant genera. Whey harbored an exceptionally high abundance of Acetobacter (21.6%), highlighting its valorization potential. Factory-scale production yielded the lowest mold and coliform counts in finished products despite higher initial coliform levels in industrial raw milk, reflecting the effectiveness of standardized hygiene management. In contrast, workshop-scale samples exhibited a higher relative abundance of environmental indicator bacteria, suggesting a comparatively elevated contamination risk this intermediate production scale. PICRUSt2-based functional predictions indicated stage-specific metabolic potential, including predicted enrichment of pyruvate and fatty acid metabolism in yogurt, amino acid metabolism in whey, and vitamin B6 metabolism in hurood. These findings provide a systematic microbial baseline for hurood, identify scale-specific microbiological risk profiles, and offer a foundation for targeted hygiene control and standardized production strategies.