Novel strategy to understand the aerobic deterioration of corn silage and the influence of Neolamarckia cadamba essential oil by multi-omics analysis

Silage, an anaerobic fermented feed for animals, is subjected to aerobic deterioration easily due to the activities of undesirable microorganisms. Aerobic deterioration always leads to the reduction of important nutritional components, animal performance and food safety. To better understand aerobic deterioration and the underlying mechanisms of Neolamarckia cadamba leaves (NCL) essential oil, metagenomic, metatranscriptomic, and metabolome analyses of silage and antimicrobial activity of NCL essential oil were performed. During exposure to air, whole-crop corn silage deteriorated as the temperature, pH value, yeasts and molds counts increased (p < 0.001), while lactic acid, acetic acid contents decreased (p < 0.001). Bacillales, Clostridiales, Saccharomycetales, and Eurotiales were active, which might be responsible for the aerobic deterioration of silage and the change in metabolites. NCL essential oil showed strong antibacterial ability to strains isolated from aerobically deteriorated silage including Candida glabrata, and Niallia circulans by affecting metabolism pathways. The addition of NCL essential oil increased the aerobic stability of whole-crop corn silage by preventing the decrease of acids and increase of temperature, pH value, yeasts and molds counts, and the relative abundances of Eurotiales, Saccharomycetales, Bacillales, and Eubacteriales. Genes related to metabolism including amino acid metabolism were down-regulated in NCL essential oil treatment. Differentially accumulated metabolites annotation indicated that pathways related to metabolism, especially amino acid metabolism were enriched. In summary, NCL essential oil could improve the aerobic stability of whole-crop corn silage by inhibiting metabolism activities, especially the amino acid metabolism of aerobic deterioration sponsors such as Saccharomycetales and Bacillales. This study provides deeper insight, a new target for controlling aerobic deterioration, and a theoretical basis for high-quality silage production.