Bioactive Compounds from Microalgae: Mechanistic Insights into the Regulatory and Therapeutic Potential of the Gut Microbiota

Targeting gut microbiota dysbiosis—a key driver in chronic disease—has become a major research focus. Microalgae-derived bioactive compounds, such as polysaccharides, ω-3 PUFAs, carotenoids, and phenolics, represent promising candidates owing to their structural diversity and multi-functional properties. They operate through a dual mechanism: serving as metabolic substrates for beneficial gut bacteria and directly modulating host signaling pathways. This review first systematically analyzes the epidemiological associations between gut dysbiosis and various chronic diseases. It then focuses on the multi-target regulatory potential of microalgal bioactive compounds in mediating gut microbiota-host interactions. Furthermore, it examines key strategies to enhance the production of these functional metabolites, from optimizing photobioreactor design and cultivation conditions to applying induction techniques. Despite promising prospects, challenges remain in enhancing compound bioavailability, overcoming individual heterogeneity in microbiota responses, and establishing standardized clinical evaluation systems. By integrating multi-omics technologies with synthetic biology tools, this review aims to provide innovative perspectives for developing microalgae-based functional foods and precision therapeutics, thereby bridging microbial ecology with personalized nutrition to offer sustainable solutions for chronic disease prevention and management.