Molecular Phylogenetics Reveals the Diversity of Antagonistic Fungal Endophytes Inhabiting Medicinal Plants in Nigeria

Antimicrobial resistance is a major health concern around the world. There is a need for novel antimicrobials from less-explored biological niches. In this study, fungal endophytes inhabiting Nigerian ethnomedicinal plants were isolated. The antimicrobial activity of these endophytes was investigated using agar plugs and cell-free broth assays. Endophytic fungal isolates were identified by sequencing the internal transcribed spacer (ITS) region, and molecular phylogenetics was done using molecular evolutionary genetics analysis version 11. Fifty-one fungal endophytes were recovered from medicinal plants used. Their fungus colonization frequencies vary depending on the plant parts, with the Crinum glaucum bulb having the highest colonization frequency (%CF = 96%). Several fungal genera were discovered using ITS sequencing and BLAST identity, including Aspergillus spp., Penicillium spp., Trichoderma spp., and Rhizopus spp. Using preliminary antimicrobial tests, 17 of the isolates demonstrated antimicrobial activity against at least one of the eight tested pathogens. The phylogenetic analysis of these isolates revealed that 11 of them are divergent strains, emerging as a monophyletic clade. These endophytes are reported for the first time in the Nigerian medicinal plants investigated. In conclusion, endophytic fungi associated with ethnomedicinal plants in Nigeria could be a source of new endophytes, which could lead to the development of novel antimicrobials.