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[Display omitted] • Different manufacturing processes lead to different microorganisms and nutrients in Rushan and Rubing. • Rushan could be used as an ideal model to study the environmental microorganisms. • Human activities had a profound influence into the cheese microbiota. The microbiota of cheese plays a critical role in determining its organoleptic and other physicochemical properties. Thus, assessing the composition of the cheese microbiota community would help promote the growth of desirable taxa and ultimately to optimize flavor, quality and safety. Here we measured microbial diversity, microbiota composition, short-chain fatty acids, and free amino acids in two traditional cheese-making strategies, Rushan and Rubing, processed in parallel from Lijiang, Eryuan, and Dengchuan of Yunnan province, China. We found distinct microbiota composition, and microbial diversity and richness in both Rushan and Rubing across all three regions, which were proportional to the scale of the cities where the cheeses were sampled. Furthermore, we found positive associations of Streptococcus and Acinetobacter with butyric acid, Phe and Tyr, which were negatively correlated with Lactococcus. For the first time, we provide evidence that environmental microbial contamination in cheese can be correlated with the manufacturing procedures and geographical regions. This should be paid more attention in upcoming cheese microbiota studies. [ABSTRACT FROM AUTHOR]