Microbial ecology of artisanal fresh cheese from Sinaloa: Influence of geographic terroir on diversity, functionality, and safety.

Abstract

Artisanal fresh cheese is fundamental to Mexico's heritage and economy, although its production with raw milk poses significant safety challenges. Given that the microbiota of Sinaloa cheeses and their ecological determinants remained unexplored, this study characterized their bacterial diversity and functional potential through massive sequencing of the 16S rRNA gene. Thirty samples from 10 locations along a latitudinal gradient were analyzed, V3 amplicon-based sequencing under Illumina Miniseq platform was performed, processing the data with DADA2 to infer Amplicon Sequence Variants (ASVs). The community was dominated by Proteobacteria (73.5%) and Firmicutes (25.9%). Canonical Correspondence Analysis (CCA) showed that altitude and geographic region were major drivers of microbiota structure, each explaining approximately 40% of the constrained variance, allowing the identification of a distinctive "terroir" (e.g., Marinomonas in the north, Streptococcus in the center). Genera of biotechnological interest such as Lactococcus, Lactobacillus, and Leuconostoc were found, a high prevalence of taxa associated with enteric contamination and opportunistic pathogens (Salmonella, Aeromonas, Acinetobacter) was detected. Predicted activities of microbial communities were primarily associated with core metabolic processes, including carbohydrate and energy metabolism. Predicted resistance-related functions were mainly linked to stress response mechanisms and antimicrobial peptide resistance, while virulence-associated traits were related to adhesion, biofilm formation, and iron acquisition, reflecting microbial strategies for environmental persistence and community interactions. In conclusion, this first amplicon-based characterization reveals a complex ecosystem driven by the environment, highlighting the duality of Sinaloa cheese as a reservoir of native lactic biodiversity and a source of health risks that requires immediate control strategies.