Bioprospecting Novel Antifungal Compounds from Endophytic Fungi in Tropical Forests
DOI:
https://doi.org/10.5281/zenodo.22688199Keywords:
endophytic fungi, antifungal compounds., bioprospecting, tropical forest, Candida auris, secondary metabolites, biosynthetic gene clustersAbstract
The rise of azole- and echinocandin-resistant fungal pathogens, exemplified by the global spread of
multidrug-resistant Candida auris, has narrowed an already thin antifungal pipeline and renewed interest in natural
sources of chemically novel antifungal chemotypes. Endophytic fungi, which live asymptomatically within plant
tissue and frequently produce bioactive secondary metabolites as part of their ecological interactions with the host
and competing microbes, remain comparatively underexplored relative to soil actinomycetes as a source of such
compounds. We isolated 412 endophytic fungal strains from leaf, stem and root tissue of 38 plant species across
three lowland tropical forest plots, identified isolates by internal transcribed spacer barcoding, and screened crude
extracts for antifungal activity against a panel of four clinically relevant pathogens including azole-resistant
Candida auris and Aspergillus fumigatus. Thirty-one extracts (7.5%) showed reproducible inhibitory activity in an
agar diffusion pre-screen, and eleven of these produced a minimum inhibitory concentration below 32
microgram/mL against at least one test pathogen in broth microdilution testing. Bioassay-guided fractionation of
the most active isolate, a Colletotrichum species recovered from the phloem of a Inga edulis host tree, yielded a
previously undescribed polyketide, tentatively designated nieb-1, that inhibited Candida auris growth at a minimum
inhibitory concentration of 2 microgram/mL and showed a distinct pattern of ergosterol-independent membrane
disruption relative to azole and echinocandin comparators in a time-kill assay. Whole-genome sequencing of the
producing strain identified a candidate biosynthetic gene cluster consistent with a partially reducing polyketide
synthase origin for the compound. These results support tropical forest endophytes, and Colletotrichum species in
particular, as an underexploited reservoir of chemically novel antifungal scaffolds worth pursuing alongside more
conventional actinomycete-focused discovery pipelines.
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