From the beginning of recombinant fungal biotechnology, the yeast Saccharomyces cerevisiae has been the most commonly used host organism for the production of heterologous proteins. Most developments of fungal biotechnology were initiated by work with this organism.

In recent years, other yeast species, such as Kluyveromyces lactis, Hansenula polymorpha, and Pichia pastoris, have become accessible for applications with recombinant proteins. Interestingly, in some instances, yeasts are unable to express eukaryotic genes which encode proteins that require posttranscriptional modifications (such as glycosylations). In contrast, filamentous fungi are able to synthesize some of these proteins in the fully functional form. Simultaneous with the development of molecular genetic techniques and gene transfer systems in yeast, comparable systems were established for filamentous fungi, making strain improvements feasible. Filamentous fungi have been used for decades as major producers in the pharmaceutical, food, and food-processing industries, leading to a high technical standard in fermentation processes with large-scale fermenters. This, together with the fact that many filamentous fungi possess the GRAS (“generally recognized as safe,” in terminology of the US. Food and Drug Administration) status, makes them ideal organisms for the production of recombinant proteins.

Many filamentous fungi with the GRAS status are standard organisms for large-scale fermentation, able to secrete large amounts of proteins, and therefore are ideal host organisms for the production of recombinant proteins. Included in this category are Aspergillus niger, Aspergillus oryzae, Acremonium chrysogenum, Penicillium chrysogenum, and Trichoderma reesei, among others.