Indigenous aseel chicken-derived probiotics as biofactories of antifungal metabolites to control mycotoxin contamination in poultry feed

Background: Fungal and mycotoxin contamination threaten poultry health, feed safety, and global food security. Mycotoxins result in reduced poultry growth, nutrient absorption, and a compromised immune system, causing severe financial losses. The rise of antibiotic resistance due to excessive antibiotic use in poultry also necessitates alternative strategies. Methods and results: Total 28 strains were isolated from the gut of indigenous Aseel and broiler chickens. Strains SB1, SB2, and SD2 completely inhibited Aspergillus flavus, Aspergillus ochraceus, and Fusarium proliferatum and were assessed via spore germination and mycotoxin reduction assays. The strains significantly inhibited fungal spore germination (up to 91.7 ± 0.3%;P ≤ 0.001) and reduced aflatoxin, ochratoxin, and fumonisin production by 91.6 ± 1.2%, 93.6 ± 0.6%, and 93.0 ± 0.5%, respectively. FTIR analysis of bacterial metabolites revealed shifts in peaks at 1467–3240 cm^{− 1}, indicating the presence of various functional groups. LC-MS/MS metabolomics, supported by multivariate analysis, revealed that metabolites were enriched with antifungal and mycotoxin-reducing compounds, including phenylacetic acid. Metabolites showed zones of inhibition up to 38.0 ± 1.1 mm against A. flavus, up to 36.0 ± 0.5 mm against A. ochraceus, and up to 34.0 ± 0.5 mm ZOI against F. proliferatum (P ≤ 0.0001). They also showed the lowest minimum inhibitory concentrations and fungicidal concentrations between 3 and 5 µLmL^{− 1} (P ≤ 0.001). 16 S rRNA sequencing identified SB1 as Bacillus subtilis (PV569530), SB2 as Bacillus clausii (PV569531), and SD2 as Bacillus sp. (PV569532). Conclusion: Thus, this study highlights the microflora of indigenous Aseel chickens as a potential source of antifungal and mycotoxin-reducing compounds, offering a sustainable approach to control fungal and mycotoxin contamination in poultry feed. Clinical trial number: As this study did not involve higher animals, no clinical trial number was required.