Maize silage serves as a crucial feed resource for ruminants, yet its quality is frequently compromised during storage by spoilage-associated microbial activity. Clostridium species, particularly Clostridium beijerinckii, are known to induce spoilage by altering fermentation pathways. This study aimed to elucidate the effects of inoculation with C. beijerinckii SHZ-8 on microbial succession, metabolite profiles, and fermentation quality in whole-crop maize silage throughout the spoilage process. Silage samples were prepared with and without C. beijerinckii SHZ-8 inoculation. Microbial community dynamics were assessed via 16S rDNA sequencing, while metabolite alterations were characterized using untargeted metabolomics. Fermentation parameters including nutrient composition, bacterial counts, and organic acid concentrations and ratios were also determined. Correlation analyses between key metabolites and core microbial taxa were conducted. Inoculation with C. beijerinckii SHZ-8 significantly reduced dry matter content by 5.28% (p < 0.01) and lactic acid bacteria counts by 54.51% (p < 0.01), while increasing Clostridium abundance by 3.40 log₁₀ CFU/g FW (p < 0.01). The dominant fermentation mode shifted from homofermentation to heterofermentation, accompanied by an 81.6% decrease in the lactate-to-acetate ratio (p < 0.01). D-galacturonic acid levels exhibited a strong positive correlation with C. beijerinckii SHZ-8 abundance (R² = 0.87, p < 0.01), suggesting its potential as a biomarker for Clostridium overgrowth. Notably, octanal and D-galacturonic acid emerged as candidate biomarkers in the inoculated group, providing a basis for the development of silage quality monitoring tools. These findings offer valuable insights for improving silage management strategies, enhancing feed preservation, and advancing the sustainability of livestock production.

This study investigated whole-plant maize at three harvest stages: one-third milk line (ML, 1/3 ML), two-thirds ML (2/3 ML), and the mature stage. Two packing densities were applied: 350 kg/m³ (low-density group) and 700 kg/m³ (high-density group). Results showed that starch content increased significantly as the maize matured. The 2/3 ML stage exhibited a 34.0% increase in starch content compared to the 1/3 ML stage (27.96 g/kg dry matter: DM vs. 20.87 g/kg DM, p < 0.01), while the mature stage showed a 13.4% increase compared to the 2/3 ML stage (31.70 g/kg DM vs. 27.96 g/kg DM, p < 0.01). After 60 days of ensiling, DM loss was significantly lower in the high-density group compared to the low-density group (3.37% vs. 9.39%, p < 0.05). From day 7 to day 60 of fermentation, the lactic acid content in the high-density group was consistently higher than in the low-density group by 14.29%, 10.00%, 8.33%, and 9.68%, respectively (p < 0.01). The relative abundance of Clostridium in both groups gradually increased during the first 30 days of fermentation, peaking on day 30 (0.05% in the high-density group vs. 0.12% in the low-density group, p < 0.05), and declined thereafter. On day 30, the abundance of Ruminiclostridium was significantly lower in the high-density group compared to the low-density group (0.12% vs. 0.40%, p < 0.05). Clostridium was negatively correlated with lactic acid bacteria (R² = −0.58, p < 0.01). It also showed negative correlations with pH, lactic acid, and acetic acid (R² = −0.25, −0.23, and −0.09, respectively; p > 0.05), but a positive correlation with ammoniacal nitrogen (R² = 0.28, p > 0.05). In conclusion, the 2/3 ML stage is the optimal harvest time for whole-plant maize. Additionally, a higher packing density can suppress spoilage-associated Clostridium and enhance silage quality.