Evaluation of Untargeted Metabolomic and Mycotoxin Profiles in Corn Silage and High-Moisture Corn

Corn silage (CS) and high-moisture corn (HMC) represent fundamental ingredients in ruminant diets; however, their chemical complexity and susceptibility to mycotoxin contamination pose challenges for feed safety and quality assessment. This study applied an innovative approach combining untargeted metabolomics and mycotoxin profiling through ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) to characterize the chemical profiles of CS (<i>n</i> = 19) and HMC (<i>n</i> = 13) samples collected from four farms in northern Italy over a period of two years. Fumonisin B1 (FB1) emerged as the most prevalent mycotoxin, with contamination levels significantly higher in HMC than CS, though all the detected levels complied with European Union (EU) guidance limits. Untargeted metabolomics distinguished CS and HMC based on their metabolic signatures: polyamines, amino acids, peptides, and phenolic acids typified CS, while HMC was primarily characterized by flavonoids and mycotoxins. Geographical origin significantly influenced both mycotoxin patterns and metabolite profiles, while the sampling season showed no significant impact. This study highlights the complementary value of metabolomics and mycotoxin screening to assess feed quality, identify biomarkers, and unravel the link between fungal contamination and biochemical composition, offering a robust strategy to support feed safety management in livestock production.