Dynamic Analysis of Fermentation Quality, Microbial Community, and Metabolome in the Whole Plant Soybean Silage

Soybean (<i>Glycine max</i> (L.) Merr.) is an important oilseed crop, known for its rich nutritional content and high-quality protein. To address the shortage of feed protein resources and better utilize soybeans as a raw material, this study investigated the feasibility of using whole-plant soybean (WPS) as silage. As the ensiling period is a critical fermentation parameter, identifying the optimal fermentation duration was a key objective. The research involves fermenting WPS for silage production, conducted over five fermentation durations: 7, 15, 30, 60, and 90 days. The fermentation quality, microbial community, and metabolome of WPS silage were analyzed across these different time points. WPS silage fermented for 30 days exhibited optimal fermentation characteristics, with the highest lactic acid (LA) content observed at 30 days (<i>p</i> < 0.05), while butyric acid (BA) was detected only at 60 and 90 days. At 30 days, <i>Enterococcus</i> genera reached its peak relative abundance and was identified as the dominant genus. Random forest analysis highlighted <i>Pantoea</i> genera as the most influential biomarker. Metabolomic analysis revealed that the metabolic pathways involved in the biosynthesis of essential amino acids valine, leucine, and isoleucine were significantly enhanced during the later stages of fermentation compared to the earlier stages. Under natural fermentation conditions, the optimal fermentation period for WPS silage is approximately 30 days. These findings provide a theoretical basis for the utilization of WPS and the subsequent optimization of fermentation quality.