PCR-DGGE analysis of fungal community in manufacturing process of a traditional Iranian cheese

The microbial communities of traditional milk-based food are of great importance in its manufacturing process, especially when using raw milk with natural cultures. Liqvan (Lighvan or Levan) is a traditional Iranian buried cheese, which is made from raw ewe´s milk without a starter addition. The aim of this study was to explore the fungal active population during this cheese manufacturing process by comparing DNA and RNA based culture independent method Denaturing Gradient Gel Electrophoresis (DGGE).
Four samples of each milk, curd and ripened cheese were collected from Liqvan village located in East Azerbaijan province of Iran. Total DNA and RNA of each sample were extracted and PCR amplicons of D1 region of 26S rRNA gene was targeted for DGGE analysis. This method applied at both DNA and RNA levels in order to examine which taxonomic groups of fungi are active at each step of ripening.
DGGE profiles of yeast amplicons showed different results between extracted DNA and RNA during ripening process. However, the main group that is present in all stages of ripening process belongs to the genus Candida although Kluyveromyces, Pichia, Galactomyces, Saccharomyces and Cryptococcus are most abundant fungi.
As no starter culture added to Liqvan cheese it seems fungal diversity are mainly rely on the indigenous microbiota of milk. Furthermore, the percentage of the dominant fungal genera from the total sequences differed among DNA and cDNA libraries.