Novel strategy to improve the ensiling quality of whole-plant sweet sorghum inoculated with Pichia anomala: Comparison with conventional Lactobacillus plantarum by microbiome and metabolome

This study examined the effects of L. plantarum (LP) and P. anomala (PA) on the fermentation characteristics, microbial community and metabolites profile of whole-plant sweet sorghum. After 14 days of ensiling, both LP and PA silages significantly improved fermentation quality, with pH dropping below 4.10 and lactic acid content increasing dramatically. Notably, PA silages exhibited elevated acetic (40.24 g/kg DM) and propionic acid (1.20 g/kg DM) levels compared to LP silages. At the phylum level, the predominant bacterial shifted from Proteobacteria (＞80%) to Firmicutes after ensiling. At the genus level, the relative abundance of Lactobacillus significantly increased to 45.57% in PA and 23.92% in LP silages, while that of spoilage genera such as Pantoea and Klebsiella showed a significant decrease. Notably, Lactobacillus_brevis became the dominant species in both LP (27.79%) and PA (27.67%) silages. Different metabolic profiles were observed between LP and PA silages. LP silages primarily drive acidification through lactic acid production and reprogramming of nitrogen metabolites, while PA silages enhance carbon metabolism by metabolizing complex carbohydrates and supplying critical cofactors to sustain microbial activity. Based on multi-omics association analysis, L. plantarum and P. anomala could drive specific microbial communities and modulate their corresponding metabolic patterns to improve the bioconversion and fermentation efficiency of sweet sorghum. • Impact of additives on silages was revealed via microbiomics and metabolomics. • Both LP and PA altered microbiota, resulting in dominant Lactobacillus_brevis . • P. anomala improved ensiling quality by antimicrobial and antioxidant metabolites. • P. anomala is a promising silage additive to improve silages quality.