Conceptual and methodological approaches applied to assessing plant food byproducts as prebiotics: a critical review of evidence and gaps

Growing interest in microbiota-directed nutrition has intensified the evaluation of plant food byproducts as potential prebiotics. However, the evidence supporting these effects depends strongly on the conceptual definitions and methodological approaches applied to characterize prebiotic activity. This review provides a critical synthesis of the evolution of the prebiotic concept and the experimental conditions used to assess plant food byproducts, integrating compositional features, <i>in vitro</i> fermentation parameters, <i>in vivo</i> designs, and analytical criteria. <i>In vitro</i> studies consistently show that fruit-, seed-, grain-, and tuber-derived byproducts stimulate beneficial taxa such as <i>Bifidobacterium</i>, <i>Lactobacillus</i>, <i>Roseburia</i>, and <i>Akkermansia</i>, enhance short-chain fatty acid (SCFA) production, and support phenolic biotransformation. These outcomes, however, are highly influenced by inoculum origin, fermentation systems, substrate dose, and physicochemical properties of the native plant matrix. Animal studies report improvements in intestinal barrier function, inflammation, and metabolic regulation, although inconsistencies in dosing and reporting limit comparability. Despite promising microbial and physiological effects, methodological heterogeneity prevents many substrates from being conclusively classified as prebiotics. Standardized characterization, multi-omics integration, advanced dynamic gut models, and well-designed clinical studies are needed to confirm efficacy and safety. Overall, plant food byproducts remain compelling candidates for prebiotic development, provided that their evaluation follows robust, consistent methodological frameworks.