Valorizing Date Fruit Byproducts into Gut-Modulating Substrates: Metabolomic Profiling and In Vitro Insights

• Valorization of date seed and pomace as sustainable prebiotic sources with metabolic and immune-enhancing potential. • DS and DP extracts promoted strain-specific probiotic growth and SCFA profiles, notably in B. bifidum and L. acidophilus . • SCFA exhibited strong antimicrobial effects against common foodborne pathogens. • UHPLC-QTOF metabolomics revealed key gut-beneficial compounds like hydroxyvalerenic acid, galactobiose, and coumarin. • SCFAs selectively inhibited COX-2, suggesting anti-inflammatory potential without COX-1 side effects. • Supports the development of synbiotic products from food waste, aligning therapeutic value with sustainability goals. This study investigates the prebiotic potential of date seed (DS) and date pomace (DP), two major agro-industrial byproducts, using a combined metabolomic and functional approach. Untargeted LC–MS profiling revealed distinct metabolite patterns in the two byproducts: DP showed a greater proportion of soluble sugars and carbohydrate-derived organic acids, whereas DS showed a broader distribution of antioxidant-, aromatic-, and lipid-associated metabolites. In vitro screening with four probiotic strains showed that Bifidobacterium bifidum exhibited the highest viability in 2% DP and produced the highest levels of fermentation-derived short-chain fatty acids (SCFAs). Lactobacillus acidophilus demonstrated optimal growth in 3% DS. SCFAs from DP– B. bifidum cultures displayed antimicrobial activity against common food-borne Gram-negative pathogens ( Salmonella MIC₈₀ = 280 µg/mL) and selectively suppressed cyclooxygenase-2 (COX-2), suggesting anti-inflammatory properties. These findings position DS and DP as sustainable gut-modulating substrates that selectively support probiotic growth and SCFA production, suggesting that date-processing waste can be converted into functional ingredients with gut-modulating, antimicrobial, and anti-inflammatory potential.