Whole-genome analysis of rice-plant-derived Enterococcus faecalis YMA3 and its effects on fermentation quality, microbial community, and metabolome of rice straw silage

Rice straw is an abundant agricultural byproduct in China, but its low nutritive value and poor natural fermentability restrict its largescale application as ruminant forage. Autochthonous lacticacid bacteria isolated from riceplant surfaces show superior environmental adaptability relative to commercial exogenous strains and represent promising candidates for silage inoculation. This study aimed to characterize an indigenous Enterococcus faecalis YMA3 originating from rice plants and explore its effects on ricestraw silage. Wholegenome sequencing, hemolysis assay, and antimicrobial susceptibility testing were performed to evaluate its genetic traits and safety. A silageensiling trial comprising a blank control, YMA3, and four commercial lacticacidbacteria treatments was conducted to assess fermentation and nutritional performance. Of these treatments, the blankcontrol and YMA3inoculated samples were selected for bacterial community and untargeted metabolomic analyses. Our results showed that YMA3 inoculation effectively reduced silage pH, enhanced lacticacid accumulation, alleviated protein degradation, and decreased fiber fractions. Higher bacterial αdiversity was maintained in the latestage silage, and Pediococcus became the predominant bacterial genus. Metabolomic profiling identified marked accumulation of nicotinamide, taurine, and multiple phenylpropanoidderived secondary metabolites linked to antioxidant capacity and feed functional properties. Genomic analysis revealed that E. faecalis YMA3 possessed complete homolactic fermentation pathways and abundant carbohydrateactive enzymecoding genes. Notably, several homologues of virulence and antibioticresistancerelated genes were predicted at the genomic level, even though the strain exhibited a γhemolytic phenotype. Collectively, E. faecalis YMA3 improved ricestraw silage quality by reshaping bacterial community structure and remodeling metabolite profiles. Further multitimepoint dynamic monitoring, invitro genefunction validation, and animalbased safety evaluations are necessary prior to practical field utilization of this strain as a silage inoculant.