Substrate-driven shifts in microbial communities reshape metabolite profiles during soybean residue fermentation

Fermentation is an effective strategy to prolong the shelf life of soybean residue and improve its value as an animal feed resource. To investigate the influence of differing fermentation conditions on the microbial community and metabolite profile of fermented soybean residue, fresh soybean residue was fermented in sealed anaerobic bag using a mixed inoculum comprising Bacillus subtilis, Lacticaseibacillus rhamnosus, Limosilactobacillus reuteri, and Lactiplantibacillus plantarum, with varying levels of wheat bran supplementation (0-15%), fermentation temperatures (24-37 °C), and durations (24-72 h). The microbial community and metabolite profiles were analyzed after fermentation. The results indicated that wheat bran supplementation was the primary factor driving microbial community shift (explaining 49.1% of the axes contributions, P = 0.002), inducing a transition from Proteobacteria-dominated to Firmicutes-dominated communities. The shift was characterized by targeted enrichment of Bacillus and multiple genera of lactic acid bacteria, alongside suppression of potential pathogens, such as Enterobacteriaceae and Pseudomonas. Concurrently, the process of fermentation resulted in a substantial increase in the levels of functional metabolites, including tryptophan, indolelactic acid, and various phenolic acids, accompanied by a reduction in flavonoid content. Fermentation temperature was the primary factor influencing metabolite distribution, explaining 18.1% of the axes contributions (P = 0.002). Network analysis revealed close correlations between specific microbiota (e.g., Lactobacillus, Limosilactobacillus) and key metabolites, including aromatic lactic acid metabolites. The findings presented herein provide insights into substrate-driven microbial modulation during soybean residue fermentation, thus establishing a foundation for optimizing fermentation conditions to enhance feed quality for animal health applications.