Engineering food systems for microbiome stability and metabolic health in deep-space missions

Background: Future long-duration human spaceflight is challenged by a complex exposome involving microgravity, ionizing radiation, circadian disruption, and highly processed space diets. To ensure multi-year shelf stability without refrigeration, current space foods rely heavily on severe processing and stabilisation strategies that impair food matrix integrity and markedly reduce microbiota-accessible carbohydrates (MACs). Beyond simple nutrient loss, this structural and fermentable substrate depletion may disrupt the diet–microbiome axis and amplify spaceflight-associated metabolic, immune, and neurobehavioral dysregulation. Scope and approach: This review examines deep-space nutrition from an interdisciplinary food science and technology perspective, with particular emphasis on how food processing, matrix design, and delivery systems shape host–microbiome interactions under extraterrestrial conditions. Current evidence on structural food design, precision nutrient delivery, and microbiome-targeted strategies, including probiotics, synbiotics, and postbiotics, is critically discussed. Particular attention is given to engineering feasibility under mission constraints, including non-thermal preservation, microencapsulation, ultra-high-barrier packaging, controlled nutrient release, and autonomous in-situ biomanufacturing for future planetary habitats. Key findings and conclusions: Conventional space nutrition strategies, which primarily focus on passive nutrient replacement, are unlikely to maintain metabolic and microbial homeostasis during prolonged missions. A transition toward active, structure-guided nutritional engineering is therefore needed. Rebuilding food matrix architecture to enable controlled and site-specific MAC delivery, together with chrononutrition-informed feeding design, may provide a practical framework for sustaining microbiome functionality in space. Among currently available intervention options, process-resilient postbiotics and biopolymer-embedded synbiotic systems appear especially promising because of their superior stability, safety, and deployability in deep-space environments. However, their implementation depends on overcoming major food engineering bottlenecks in processing, encapsulation, packaging, and autonomous production. Integrating functional food design with host–microbiome precision nutrition may thus provide a technological and biological foundation for sustainable human exploration beyond Earth.