# The predominance of Penicillium, Mucor, and Yarrowia among spoilage fungi in cultured dairy products produced by 3 manufacturers, as revealed by amplicon sequencing

## TL;DR

This study identifies Penicillium, Mucor, and Yarrowia as the main fungi causing spoilage in dairy products like yogurt and sour cream.

## Contribution

The study reveals the predominance of specific spoilage fungi in dairy products using DNA sequencing and compares genetic variation across genera.

## Key findings

- Penicillium was the most frequently isolated genus, regardless of preservative use.
- The 5.8S rDNA region showed significant variation in Candida but not in most other genera.
- ITS sequencing proved more effective than morphology for fungal identification.

## Abstract

Summary: Spoiled cultured dairy products (yogurt, cottage cheese, and sour cream) were collected and plated to isolate fungal cultures. We extracted DNA from the fungi, and PCR was performed on the ITS1-5.8S-ITS2 ribosomal DNA (rDNA) region. The Sanger sequencing results were used to identify the genera to which the fungal isolates belonged. The 3 most common genera identified were Penicillium, Mucor, and Yarrowia. Additionally, 483 fungal isolates related to cultured dairy products were downloaded from FoodMicrobeTracker and combined with the sequences from this study to compare the amount of variation in the 5.8S rDNA subregion.

Summary: Spoiled cultured dairy products (yogurt, cottage cheese, and sour cream) were collected and plated to isolate fungal cultures. We extracted DNA from the fungi, and PCR was performed on the ITS1-5.8S-ITS2 ribosomal DNA (rDNA) region. The Sanger sequencing results were used to identify the genera to which the fungal isolates belonged. The 3 most common genera identified were Penicillium, Mucor, and Yarrowia. Additionally, 483 fungal isolates related to cultured dairy products were downloaded from FoodMicrobeTracker and combined with the sequences from this study to compare the amount of variation in the 5.8S rDNA subregion.

•Fungi cause spoilage in cultured dairy products, with or without preservatives.•Penicillium, Mucor, and Yarrowia were most commonly isolated and identified.•Internal transcribed spacer sequencing can be used to identify fungal isolates better than morphology alone.•Amount of variation between 5.8s rDNA subregions depends on the genus.

Fungi cause spoilage in cultured dairy products, with or without preservatives.

Penicillium, Mucor, and Yarrowia were most commonly isolated and identified.

Internal transcribed spacer sequencing can be used to identify fungal isolates better than morphology alone.

Amount of variation between 5.8s rDNA subregions depends on the genus.

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.