Molecular Characterization and Phylogenetic Studies of Fungal Species in Piggeries and Implications for Mycotoxin Contamination and Food Safety

Background Fungal contamination in animal feed poses serious risks to animal health, food safety, and public health. Fungi such as Aspergillus, Fusarium, and Penicillium can produce mycotoxins, which impact livestock and human health. This study aimed to isolate and molecularly characterize fungal species in pig feed and faeces from registered and unregistered farms in Lagos State, Nigeria. Eighteen samples (6 feed and 12 feces) were collected and refrigerated before culturing on Sabouraud Dextrose Agar at 28°C for 5-7 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 analysis assessed genetic similarity. Results Results showed that fungal contamination was more frequent in faeces collected from unregistered farms than registered farms. Microfungi belonging to the genera Aspergillus , Pichia , Rhizopus , and Trichoderma were isolated and purified from feed while Aspergillus and Candida genera were isolated and purified from faeces. Molecular analyses revealed high genetic similarity among isolates, with Aspergillus flavus and Rhizopus arrhizus showing 100% identity with known strains. All 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. Conclusions The occurrence of mycotoxin-producing fungi in pig farms, emphasizes the need for strict monitoring to enhance food safety.