Bacterial communities in colonial cheese samples from Vale do Taquari, RS, Brazil

Colonial cheese, a traditional Brazilian artisanal product of considerable cultural and economic significance in southern Brazil, is still poorly characterized regarding its sensory quality, microbial ecology, metabolite composition, and microbiological safety. This study characterizes colonial cheeses from the Vale do Taquari region (Rio Grande do Sul, Brazil) by integrating sensory evaluation with microbiological, compositional, and multi-omics analyses. Four cheeses from diverse producers were evaluated for sensory acceptance, centesimal composition, and microbiological compliance with Brazilian regulations. Using 16S rRNA gene metabarcoding, we analyzed prokaryotic community structures, complemented by metabolite profiling via liquid chromatography coupled with high resolution mass spectrometry (LC-HRMS). Findings revealed that cheeses produced under industrial conditions exhibited higher sensory acceptance and reduced microbial diversity, dominated by Streptococcus and Lactococcus. In contrast, artisanal cheeses showed greater microbial diversity with significant contributions from Lactobacillus and non-starter taxa. Metabolomic analysis identified terpenoids, phospholipids, fatty acids, and phenolic compounds linked to microbial composition and sensory attributes. Notably, one artisanal sample presented microbiological non-compliance, including Listeria monocytogenes. Multivariate analyses highlighted strong associations among microbial communities, metabolite profiles, physicochemical parameters, and sensory acceptance. These insights emphasize the role of microbial ecology in the quality and safety of colonial cheeses, advocating for improved starter cultures and hygienic practices to enhance traditional Brazilian artisanal products.