ResultsThe Poria cocos fermentation broth at 2.5% significantly enhanced the total number of L. plantarum R9 (p = 0.001) and L. gasseri B1-27 (p = 0.013) after 20 h of fermentation, and Non-targeted metabolomics assays conducted before and after fermentation of the human milk-derived L. plantarum R9 and L. gasseri B1-27 using the 2.5% Poria cocos fermentation broth revealed 35 and 45 differential metabolites, respectively. A variety of active substances with physiological functions, such as L-proline, L-serine, beta-alanine, taurine, retinol, luteolin, and serotonin, were found to be significantly increased. Mannitol, a natural sweetener with a low glycemic index, was also identified. The most significantly altered metabolic pathways were pyrimidine metabolism, pentose phosphate, yeast meiosis, ABC transporter, insulin signaling, and mineral absorption, suggesting that co-fermentation of human milk-derived probiotics and Poria cocos may affect the metabolism of trace minerals, sugars, organic acids, and amino acids.