Transformation of Agro-Industrial By-Products into High-Value Animal-Derived Foods: Bioactive Compounds, Microbiome-Mediated Biotransformation, Metabolomic Traceability and Circular Valorization

Agro-industrial by-products are increasingly considered as feed resources for circular animal production, but their value should not be interpreted only as a low-cost replacement of conventional ingredients. This scoping review critically examines how by-products from grape, olive, tomato, citrus, cereal, brewery, oilseed and vegetable processing chains may contribute to the development of high-value animal-derived foods. Particular attention is given to bioactive compounds, polyphenols, carotenoids, tocopherols, fermentable fibres and residual lipids, as well as to microbiome-mediated biotransformation, host metabolic pathways, compound transfer, product-quality modulation, feed safety and circular valorization. Available evidence indicates that selected by-products can influence milk, cheese, meat, eggs and fish products by modifying fatty acid profile, oxidative stability, antioxidant-related traits, pigmentation, volatile compounds, shelf-life and, in some cases, the transfer of specific metabolites to edible products. However, these responses depend on by-product source, processing method, inclusion level, active dose, animal species, basal diet and analytical endpoints. Chemical richness alone is therefore insufficient to support functional claims. Stronger evidence requires studies that connect matrix characterization, processing stability, microbial and host-mediated transformation, biological intermediates and final product quality within the same experimental design. Precision circular feeding should therefore combine local availability, safety, active-dose definition, metabolomic and lipidomic traceability, and product-level validation to support reproducible improvements in high-value animal-derived foods.