Genomic insights into Enterococcus faecalis YMA3 and Its Impact on Rice Straw Silage Quality, Microbial community, and Metabolome

Background Rice straw is an abundant agricultural byproduct whose use as ruminant feed is constrained by its recalcitrant lignocellulosic structure and low digestibility. Here, we evaluated a novel autochthonous strain, Enterococcus faecalis YMA3, as a silage inoculant to improve rice straw fermentation quality and nutritive value. Results A multi-omics framework integrating whole-genome sequencing (WGS) of E.faecalis YMA3 with full-length 16S rRNA gene sequencing and untargeted metabolomics of silage were applied. Genomic analysis indicated genetic capacity for homolactic fermentation, carbohydrate utilization and putative fiber-related substrate degradation (carbohydrate-active enzyme genes), and antimicrobial activity including a Class III bacteriocin. YMA3 significantly accelerated acidification (final pH 4.02), increased lactic acid (6.46% DM), associated with reductions in neutral detergent fiber (NDF) and acid detergent fiber (ADF). E.faecalis YMA3 reshaped microbial succession, enriching Pediococcus (76% relative abundance) and suppressing undesirable Enterobacteriacea e such as Klebsiella and Enterobacte r. Metabolomics confirmed extensive biochemical remodeling with marked accumulation of nicotinamide and taurine and enrichment of phenylpropanoid and isoflavonoid biosynthesis pathways. Conclusions E.faecalis YMA3 acted as an effective starter culture that coordinates rapid acidification, community restructuring, and functional metabolite formation.