Traditional Portuguese cheeses are highly valued for their unique organoleptic properties and quality. These properties stem from using raw, instead of pasteurized, milk in their production, which has a very diverse and rich microbiota. To ensure the quality of the cheeses, some traditional cheeses deserve a protective designation to guarantee their authenticity and adherence to traditional manufacturing practices - Protected Designation of Origin (PDO), which ensures that the products are produced, processed, and prepared in a defined geographical area, using traditional manufacturing methods and ingredients specific to that region. This FCT project, EMOTION, collected, in 2021, a total of 24 cheese samples, sixteen of which were collected from four PDO cheese factories in Azeitão and eight collected from two PDO cheese factories in the Nisa. In this master’s project, to find differences in the microbiota present in the two types of cheese, multivariate data visualization methods were used, such as Principal Coordinate Analysis (PCoA) and Non-metric Multidimensional Scaling (NMDS), as well as two statistical tests, Permutational Multivariate Analysis of Variance (PERMANOVA) and Analysis of Similarities (ANOSIM). The second objective was to identify the bacteria responsible for differentiating the two types of cheese. For this, a method known as Linear Discriminant Analysis Effect Size (LEfSe) was used. Both tests, PERMANOVA (p = 0.039) and ANOSIM (p = 0.004), revealed significant differences in the microbial composition of Nisa and Azeitão PDO cheeses. Based on the LDA scores histogram, bacteria of the genus Lacticaseibacillus (p = 0.0433) have a higher abundance in Nisa PDO cheeses than in Azeitão cheeses. Bacteria of the genera Enterococcus (p = 0.00117), Corynebacterium (p = 0.00705), and Latilactobacillus (p = 0.000757) have a higher abundance in PDO cheeses from the Azeitão region.

Trabalho de projeto de mestrado, Bioestatística, 2024, Universidade de Lisboa, Faculdade de Ciências