As all the DNA present in the cheese samples is sequenced, the high throughput sequencing may detect any type of DNA (bacteria, archaea, eukaryotes and viruses), provided that adequate references are used. Eukaryotes, such as Geotrichum candidum, Debaryomyces hansenii, and Penicillium roqueforti, were found, which was not surprising, as these fungi are frequently used in cheesemaking.