Schizochytrium spp. as Multi-Product Marine Biofactories for Health and Nutritional Applications: Mechanisms and Future Biorefinery Perspectives

Schizochytrium spp. and related thraustochytrids are heterotrophic marine protists that have emerged as promising microbial platforms for the production of high-value lipids and bioactive metabolites. Although industrial applications have primarily focused on DHA-rich single-cell oils, these organisms possess broader biosynthetic capabilities, including the production of other omega-3 fatty acids, squalene, carotenoids, sterols, selenium-enriched biomolecules, proteins, extracellular enzymes, and exopolysaccharides. This review examines the biological characteristics, metabolic pathways, fermentation strategies, downstream processing approaches, nutritional applications, safety considerations, and future development of Schizochytrium-based production systems. DHA has the strongest nutritional evidence, particularly for neural, retinal, maternal–infant, and cardiovascular nutrition, whereas clinical evidence for disease prevention and non-DHA coproducts remains limited. Schizochytrium-derived products have potential in functional foods, infant nutrition, vegan supplements, fortified foods, cosmetics, pharmaceutical excipients, oral-vaccine platforms, and multiproduct biorefineries. Despite considerable progress, challenges including strain variability, production economics, oxidative stability, downstream purification, regulatory requirements, and product standardization remain major barriers to broader commercialization. Future advances will depend on combining strain engineering, multi-omics-guided pathway optimization, sustainable feedstocks, food-compatible extraction technologies, and integrated techno-economic and life-cycle assessments to establish Schizochytrium spp. as versatile marine biomanufacturing platforms.