Impacts of off-flavor on microbial community structure, nutritional traits and metabolite profiles in whole-plant corn silage

Off-flavor in corn silage compromises feed quality and animal performance, yet the microbial-metabolic changes driving its formation remain poorly understood. In this study, microbiome profiling, metabolomics, and sensory evaluation were integrated to elucidate the changing factors driving off-flavor formation. Silage samples from 10 dairy farms were classified by sensory score into control (CON, 15–20) and abnormal silage groups (ASG, <15). The bacterial community structure was analyzed, metabolites were identified and quantified using gas chromatography-mass spectrometry (GC-MS), and the associations between microorganisms and metabolites were explored via Spearman correlation analysis. Compared with the CON, the ASG exhibited significantly lower concentrations of dry matter ( p = 0.01), starch ( p = 0.04), lactic acid ( p = 0.03), and acetic acid ( p = 0.04), while those of neutral detergent fiber ( p = 0.02), acid detergent fiber ( p = 0.03), propionic acid ( p = 0.01), and butyric acid ( p = 0.02) were significantly higher. The pH value of the ASG was increased to 4.99 compared to that of the CON (3.74), with a significant difference observed between them. Meanwhile, the abundances of phylum Firmicutes (p-Firmicutes) and genus Lactobacillus (g-Lactobacillus) in the ASG were both significantly lower than CON. After further screening from the 32 differentially abundant metabolites (excluding 16 redundant metabolites and 2 that remained unannotated due to database limitations), a total of 14 core differential metabolites associated with off-flavor in silage were identified. Among these, compounds contributing acetic and waxy aromas were enriched in the ASG. Spearman correlation analysis showed Corynebacterium and JC017 were positively correlated with fatty and waxy compounds (methyl linoleate, oleic acid), while Massilia and Paenibacillus_D were negatively correlated with phenylacetic acid. These findings demonstrate that off-flavor in corn silage arises from Lactobacillus decline, aerobic spoilage bacteria overgrowth, and subsequent accumulation of phenylacetic acid coupled with gallic acid depletion. This microbiome-metabolomics interaction provides a mechanistic framework for developing targeted strategies to control silage off-flavors.