Beyond Fish: A Comprehensive Review of Microbiome Dynamics, Allergen Mitigation, and Biorefinery in Fermented Marine Invertebrates

<ns3:p> While fermented finfish products dominate the global discourse on marine fermentation, the indigenous fermentation of marine invertebrates, including crustaceans, bivalves, cephalopods, and echinoderms, remains a highly complex and under-researched domain of food science. This review synthesizes the current literature to highlight the phylum-specific biotechnological processes governing these foods. By analyzing distinct coastal micro-ecologies, we contrast traditional halophilic bacterial dominance with modern and unconventional processing deviations, such as sugar-assisted low-salt fermentations, sequential strain fortification of fungi and bacteria, enzymatic pretreatments, and targeted microbial consortia. We explore advanced proteolytic pathways that yield specific umami markers, functional compounds like γ-aminobutyric acid (GABA), angiotensin-converting enzyme (ACE)-inhibitory peptides, and improve the textural gelation of myofibrillar proteins. Crucially, this review addresses modern safety paradigms, detailing how targeted fermentation windows mitigate biogenic amines and how seasonal temperature fluctuations impact the proliferation of pathogens like <ns3:italic>Aeromonas</ns3:italic> spp. in bivalves. We highlight breakthrough interventions in shellfish allergy management, demonstrating how specific microbial starters (e.g., <ns3:italic>Limosilactobacillus fermentum</ns3:italic> ) and synergistic physical and chemical hurdle technologies destroy immunoglobulin E (IgE)-binding epitopes on tropomyosin. Finally, we explore the future of marine fermentation, emphasizing its evolution from spontaneous preservation into precise bio-engineering. We provide a comprehensive matrix of industrial cross-applications, discuss the circular blue economy via the green biorefinery of shell waste and shrimp heads, and introduce the critical concept of microbial heritage transfer by applying indigenous fermentation methodologies to sustainable substrates to recreate the flavors of endangered species without ecological harm. </ns3:p>