Occurrence, molecular characterization and phylogenetic studies of fungal species in piggeries and implications for food safety

Fungi are a diverse group of heterotrophic eukaryotes that play important roles in animal, plant, and environmental health. While certain species present in livestock feed contribute to nutrition and productivity, others produce mycotoxins that pose serious risks to animal health, food safety, and public health. This study aimed to isolate, identify, and characterize fungal species present in feed and faecal samples from registered and unregistered pig farms in Lagos State, Nigeria. Feed ( n = 6) and faecal ( n = 12) samples were collected, refrigerated and cultured on Potato Dextrose Agar (PDA) at 25 –28 °C for 4 days. Pure isolates were identified morphologically, and DNA was extracted. PCR amplification targeted ITS region of ribosomal DNA, with sequence comparisons made using GenBank references for species identification. Phylogenetic relationships were assessed. Results showed that fungal contamination was common in faeces (33.3% − 100.0%) and feed (100%) collected from registered and unregistered farms. Microfungi belonging to the genera Aspergillus , Pichia , Rhizopus , and Trichoderma were isolated from feed while Aspergillus and Candida genera were isolated from faeces. Molecular analyses revealed high genetic similarity among isolates, with Aspergillus flavus and Rhizopus arrhizus showing 100% identity with known strains. Four evolutionary models produced consistent phylogenetic trees, grouping the fungal species into well-supported clades, with only minor differences in branch lengths and bootstrap values. No significant genetic divergence was observed between isolates from registered and unregistered farms. The occurrence of potential mycotoxin-producing fungi in the pig farms studied offers baseline data that underscores the importance of extensive monitoring and surveillance to promote food security and protect environmental health. Not applicable.