Terminal-restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis profiling of fungal communities in Camembert cheese

Identifying and isolating yeasts and moulds within a fungal community is challenging. The main goal of the present study was to assess a new approach for the detection and identification of fungi involved in Camembert cheese rind formation to replace the use of traditional microbiological techniques. Two molecular methods, terminal-restriction fragment length polymorphism (T-RFLP) and automated ribosomal intergenic spacer analysis (ARISA), were adapted and compared for their potential to determine fungal composition directly from cheese samples. The two techniques in combination with principal component analysis showed differences in the fungal composition of cheeses when comparing surface with centre, different batches, manufacturing processes and ripening times. Moreover, cheese stabilisation induced changes in the flora at the cheese centre, and difference in size (150 g versus 1 kg) modified surface flora. Nine fungal genera were identified in cheese samples: Cladosporium, Debaryomyces, Geotrichum, Kluyveromyces, Mucor, Penicillium, Pichia, Saccharomyces and Yarrowia.