Molecular Identification and Phylogenetic Analysis of Aflatoxigenic Aspergillus Species in Stored Maize from Maiduguri, Nigeria

Fungal contamination of stored maize poses important food-safety and post-harvest quality concerns, particularly in warm environments where Aspergillus and other toxigenic fungi can proliferate. This study investigated the fungal diversity of stored maize in Maiduguri, Nigeria, and confirmed selected isolates using internal transcribed spacer (ITS) sequencing. Maize samples were collected from six warehouses representing harvest years 2021–2024, and fungi were isolated using culture-based techniques and identified morphologically. Genomic DNA from representative isolates was extracted, subjected to ITS-PCR, sequenced by the Sanger method, and compared with reference sequences in the NCBI GenBank database using BLASTn. A total of 38 fungal isolates were recovered, comprising eight species, with Aspergillus spp. accounting for 76.31% of the isolates. A. niger was the most frequently recovered species (21.05%), followed by Scopulariopsis candida (18.42%) and A. oryzae (15.79%). Fungal loads varied considerably among warehouses, ranging from 1.5 × 10⁴ to 9.8 × 10⁴ CFU/g. ITS sequencing confirmed A. aflatoxiformans, A. fumigatus, Talaromyces islandicus, A. parvisclerotigenus, and A. flavus with 100% query coverage and 99.62–100% sequence identity. Phylogenetic analysis further supported the clustering of the isolates with closely related GenBank reference strains. The predominance of Aspergillus, including members associated with aflatoxin production, highlights the potential food-safety implications of inadequate maize storage. The findings demonstrate the usefulness of combining conventional mycology with ITS-based molecular identification for characterizing fungal contaminants and support improved storage hygiene and routine surveillance of stored maize in Maiduguri.

Keywords: stored maize; fungal contamination; Aspergillus; ITS sequencing; molecular identification; phylogeny; food safety.