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No microbiomes were detected as discriminative features between STA and CON. The addition of FRU and PEC presented more peptides, such as Leu-Val-Thr, Leu-Phe, Ile-Pro-Ile, Val-Trp, and Ile-Leu-Leu but a lower abundance of metabolites for triterpene glycosides including sanchinoside B1, medicagenic acid, betavulgaroside IV, and prosapogenin compared to CON. The addition of PEC presented more phenyllactic acid compared to CON. Our study demonstrated that the addition of pectin and fructose improved the quality of alfalfa silage mainly b