Metagenomic and physicochemical analysis of the artisanal production stages of Kochkäse cheese from raw and pasteurised milk

Background, Context or Rationale Kochkäse is a Brazilian artisanal cheese of German origin, traditionally produced in the Vale Europeu region of Santa Catarina state. It is characterised by a uniform texture obtained through the natural coagulation of skim milk and subsequent cooking of the matured curd. Although pasteurisation ensures microbiological safety, artisanal producers prefer raw milk to preserve the natural microbiota and the product's unique sensory properties. Understanding the genetic and functional diversity of these microbial communities through metagenomics is essential to improve safety and maintain cultural heritage. Aim(s) To evaluate, for the first time, the metagenomic profiles of bacterial and fungal populations, as well as their physicochemical characteristics, during the production stages of Kochkäse made with raw and pasteurised milk. Methods Samples of white cheese, matured cheese (5 days) and final Kochkäse cheese were analysed for physicochemical composition (moisture, pH, lipids, proteins and ash). Microbial identification was performed using next‐generation sequencing (NGS) of the 16S ribonucleic acid‐rRNA (bacteria) and internal transcribed spacer—ITS (fungi) regions. Major Findings Kochkäse cheese presented high moisture and low fat content. Metataxonomic analysis revealed that Streptococcus thermophilus predominated in pasteurised cheese (>80%) and Lactobacillus delbruecki i ( L. delbruecki i) in raw milk (>55%). Among the fungi, Candida tropicalis was the dominant species, especially in raw milk samples. Final cooking at 90°C proved crucial for reducing the microbial load. Scientific or Industrial Implications The results highlight that the type of milk and the rigour of manufacturing practices directly influence the microbiological identity and safety of the cheese. These data help standardise the quality and value of regional gastronomic heritage.