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Natural bioactive polysaccharides and peptides, as prebiotic components, obtained from several natural sources are considered potent modulators of gastrointestinal physiological structure, function, and health especially through the management of inflammatory bowel diseases, immunomodulatory effects, and certain beneficial actions on the gut microbiota and their metabolites. Therefore, more studies in this important area are required to determine the structural features of functional biopeptides and bio-polysaccharides, accurate dosage for therapeutic applications, gut microbiota, and metabolites changes in the intestine as well as to decipher the mechanism-of-action occurring in the gut upon the consumption of these bioactive components.