Rice Epiphytic Strain Enterococcus faecalis YMA3 Improves Corn Stover Silage Quality via Metabolic Regulation Without Shifting the Bacterial Community

Corn stover serves as a key roughage for ruminants, but poor preservation limits its nutritional value. This study evaluates whether E. faecalis YMA3, an epiphytic strain from the rice phyllosphere, can improve corn stover silage preservation compared with a commercial E. faecalis strain F and an untreated control. We inoculated chopped corn stover with YMA3, strain F, or sterile water, and ensiled the mixtures in vacuum bags for 1, 7, 15, and 45 days. At each time point, we measured fermentation parameters, chemical composition, microbial counts, and aerobic stability and performed untargeted metabolomics on day 45. Both inoculants enhanced preservation relative to the control, as evidenced by higher crude protein content and lactic acid bacteria counts, as well as lower pH, NH3-N, and aerobic bacteria counts. Notably, YMA3 outperformed strain F in reducing aerobic bacteria and NH3-N levels. Metabolomic analysis identified 309 differential metabolites between YMA3-treated and control silage, including elevated phosphatidylcholine, tauroursodeoxycholic acid, and 3,4-dihydroxyphenylpropionic acid, along with enriched glycerophospholipid, amino acid, and fatty acid metabolism pathways—changes that may underpin improved preservation. In conclusion, E. faecalis YMA3 acts as an effective microbial inoculant for corn stover silage, outperforming commercial strain F in protein preservation and aerobic stability by modulating bacterial microbiota and metabolic characteristics. Given the limitation that we tentatively annotated metabolites based on spectral matching rather than authentic standards, follow-up research needs to validate key differential metabolites and evaluate their feeding effects in animal trials. This work provides a preliminary foundation for developing novel microbial feed additives in ruminant production.