In vitro gastrointestinal digestion and its effects on the chemical-structural reprogramming and bioaccessibility of bioactive compounds and macronutrients from native Brazilian fruits

Native Brazilian fruits are rich in phenolic compounds, carotenoids, anthocyanins, proteins, and minerals; however, their functional value depends on the transformations that occur during gastrointestinal digestion, and not only on their initial composition. This review evaluates how in vitro models of gastrointestinal digestion, particularly static systems (INFOGEST) and dynamic platforms (e.g., TIM, DIDGI, SHIME), influence the bioaccessibility and chemical-structural reprogramming of bioactive compounds in different matrices (pulp, peel, seeds, flours, and agro-industrial by-products). By integrating evidence from studies employing harmonized and non-harmonized protocols, the review clarifies how methodological differences affect comparability, compound release, and the interpretation of bioaccessibility data. Evidence demonstrates that digestion induces matrix-dependent transformations, including the depolymerization of phenolic compounds, the degradation of anthocyanins at intestinal pH, and the micellization-dependent release of carotenoids. These processes often reduce overall antioxidant capacity after the intestinal phase but simultaneously generate low-molecular-weight metabolites with enhanced solubility and biological specificity, exhibiting anti-inflammatory and enzyme-inhibitory effects. Furthermore, protein digestibility and mineral bioaccessibility are influenced by structural organization, maturation stage, and matrix interactions. Unlike previous reviews focused primarily on compositional data or isolated compound classes, this work provides an integrated, model-driven perspective connecting digestion protocols, compound classes, and food matrix effects, while identifying critical gaps, including the limited use of dynamic models, the lack of characterization of the intermediate fraction, and the underrepresentation of colonic fermentation. • Gastrointestinal digestion reprograms bioactive compounds in native Brazilian fruits • Static and dynamic in vitro models differ in predicting bioaccessibility outcomes • INFOGEST is central but limited for capturing intermediate digestive transformations • Loss of antioxidant capacity masks formation of bioactive low molecular metabolites • Advanced analytical strategies are needed beyond simple pre and post digestion