Abstract Feed shortage has hindered the development of the world’s livestock industry, and the rational use of non-conventional forages can help resolve this issue. To improve the fermentation quality of Caragana korshinskii silage, this study isolated lactic acid bacteria (LAB) from fresh Caragana korshinskii and silage samples, as alternatives to traditional commercial LAB inoculants. Utilizing Single Molecule, Real-Time (SMRT) sequencing technology and metabolomics analysis, the microbial community structure and metabolome were examined after 60 days of fermentation to elucidate the mechanism by which isolated LAB affect the fermentation quality of Caragana korshinskii silage. After 60 days of ensiling, the dominant microbial population in the silage shifted from harmful bacteria such as Erwinia, Pantoea, and Enterobacter to LAB. Compared to commercial LAB, the isolated Lactiplantibacillus plantarum significantly reduced the microbial diversity of Caragana korshinskii silage. The species composition of LAB became simpler with Lentilactobacillus parakefiri dominating and achieving a higher relative abundance. By down-regulating Butanoate metabolism and the Pentose phosphate pathway and up-regulating the Ascorbate and aldarate metabolism pathway, the isolated Lactiplantibacillus plantarum significantly lowered the pH of the silage, increased the content of water-soluble carbohydrates (WSC) and lactic acid (LA), reduced the neutral detergent fiber content (NDF), and improved in vitro neutral detergent fiber digestibility (IVNDFD), thereby enhancing the fermentation quality of Caragana korshinskii silage. On the other hand, the isolated Limosilactobacillus fermentum had the opposite effect, with its ensiling outcome being less effective than that of commercial LAB. The results of the study indicate that the addition of the isolated Lactiplantibacillus plantarum improved the quality of Caragana korshinskii silage by regulating metabolic pathways and the composition of microbes within the ensiled feed. Graphical Abstract
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