Dairy environment and seasons affect the microbiome of a traditional artisanal cheese

Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow’s milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product’s sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.