Abstract
Fungal spoilage in cultured dairy products causes consumer dissatisfaction, food waste, and financial losses. This study aimed to identify and characterize fungi responsible for spoilage in cultured dairy products by amplifying the ITS1-5.8S-ITS2 ribosomal DNA (rDNA) region. A total of 200 isolates collected from 154 spoiled dairy products, including yogurt, cottage cheese, and sour cream. The most common genera identified were Penicillium (46.5% of isolates), Mucor (15% of isolates), and Yarrowia (12.5% of isolates). Penicillium remained the most frequently isolated fungal genus regardless of the inclusion of preservatives in the dairy products. The internal transcribed spacer (ITS) sequences from this collection and ITS sequences from an additional 483 fungal isolates from cultured dairy downloaded from FoodMicrobeTracker were aligned to assess sequence diversity in their 5.8S rRNA regions. All isolates in more than half (9/15) of the genera did not differ by an SNP in their highly conserved 5.8S region. However, the aligned 5.8S rDNA region from 182 Penicillium isolates revealed 5 unique SNPs, and those from 37 Mucor isolates had 11 SNP differences. The most sequence diversity was observed in Candida with 36 SNPs among 78 aligned 5.8S rDNA regions, demonstrating that variation within this region varies depending on the genus.