Improving Fungal Cultivability for Natural Products Discovery

Abstract

The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.

Predicting global numbers of teleomorphic ascomycetes

“…Fungi occur in the soil or soil-associated environments at least for some stage in their life-cycle known as soil fungi (Bridge and Spooner 2001). They are active, freely growing fungi closely associated with other organisms or inactive dormant propagules (Rämä and Quandt 2021). The role of soil fungi are an extremely complex and are fundamental to the soil ecosystem (Hawksworth et al 1995).…”

In silico identification of multi-target inhibitors from medicinal fungal metabolites against the base excision repair pathway proteins of African swine fever virus

“…22,23 However, despite their potential, fungal secondary metabolites are still underutilized as a source of bioactive drug molecules to address veterinary diseases, including ASF. [24][25][26] Furthermore, considering the extensive biodiversity of secondary fungal metabolites, the likelihood of discovering bioactive antiviral compounds against ASFV remains substantial.…”

Discovery of Enzyme Inhibitors from Mangrove Sediment Derived Fungus Trichoderma harzianum SCSIO 41051

“…Mangrove wetland ecosystems are of the unique properties associated with high salinity, strong UV exposure, and frequent tidal fluctuations [2,3] . Therefore, the in situ cultivation of fungi from mangrove sediment has fostered the production of a diverse range of novel active secondary metabolites [4] …”