In this review, we summarised the information on probiotic bacteria and their encapsulated forms as functional food components, emphasising survival, technological effects, and product quality. Probiotics from genera such as Bifidobacterium and Lactobacillus are widely used to prevent and manage gastrointestinal and systemic disorders. However, their efficacy is often limited by the loss of viability that occurs during processing, storage, and passage through the gastrointestinal tract. In this article, we analyse the major encapsulation techniques (spray drying, freeze drying, emulsification, extrusion, coacervation, and electrospraying/electrospinning) and emphasise the important function of encapsulating materials, such as proteins, polysaccharides (e.g., alginate, pectin, and chitosan), lipids, and their combinations. Particular focus is given to mixed polymer systems and co-encapsulation with cryo- and protective agents, which can enhance resistance to acid and bile, increase survival by 1–2 log units, and help maintain bioactive compounds. We also consider fermented dairy products, cheese, meat products, and plant-based matrices as carriers for free and encapsulated probiotics. Thus, we show that, when properly selected, these systems can improve microbial stability, modulate proteolysis and lipolysis, and enhance antioxidant and antimicrobial properties without compromising sensory quality. Particular emphasis is placed on emerging plant-based beverages and alternative substrates that could enable probiotics to be consumed by lactose-intolerant and vegetarian populations. Overall, we present encapsulation as a promising strategy for designing next-generation functional foods with predictable probiotic survival and tailored technological and sensory characteristics.

Bacterial phytopathogens such as Ralstonia, Xanthomonas, and Pectobacterium pose a serious threat to global food security, while overuse of chemical pesticides has led to resistance and environmental concerns. Trichoderma, traditionally known for antifungal activity, is emerging as a versatile antagonist of bacterial diseases through antibacterial metabolites, immune response, nutrient competition, and rhizosphere modulation. Multi-omics advances have revealed novel biosynthetic gene clusters and host interaction mechanisms, while CRISPR-based genome editing and synthetic biology approaches are enabling the tailored strains with enhanced biocontrol efficiency. Nanotechnology further contributes by facilitating nanoparticle-mediated biosynthesis and controlled-release formulations, improving stability and targeted field delivery. Despite remaining challenges related to field translation, biosafety, and regulation, the integration of omics, genetic engineering, and nanotechnology establishes Trichoderma as a next-generation platform for sustainable and precision crop protection.

Radiation enteritis (RE) constitutes a catastrophic collapse of the intestinal holobiont, fundamentally constraining the curative potential of abdominopelvic radiotherapy. Current clinical management, limited by a reductionist focus on host DNA damage, often overlooks the maladaptive ecological feedback loops driving chronic pathology. This review advocates for a definitive transition from empirical probiotic supplementation to microbial synthetic biology for the rational reprogramming of the gut ecosystem. We delineate strategies for thermodynamic engineering, utilizing engineered commensals as living oxygen sinks to scavenge luminal oxygen and nitrate, thereby starving proteobacterial blooms and restoring the physiological hypoxia essential for mucosal recovery. Addressing the Akkermansia paradox, in which nutrient deprivation drives beneficial microbes toward mucin-degrading pathogenicity, we propose genetic domestication (e.g., sulfatase deletion) to decouple immunogenicity from barrier erosion. Furthermore, we explore the design of biological computers equipped with Boolean logic gates to resolve the immunological timing paradox by precisely modulating the cGAS-STING axis and reprogramming macrophage metabolism via the itaconate shunt. Integrating armored polydopamine delivery, genetic entanglement (STALEMATE) for biocontainment, and Gut-on-a-Chip validation, we outline a roadmap for colonic terraformation. This engineering-driven approach aims to actively reconstruct homeostasis, uniquely decoupling epithelial regeneration from tumor protection to improve long-term cancer survival.

Despite the widespread success of combination antiretroviral therapy (cART) in suppressing plasma viremia to undetectable levels, people living with HIV-1 (PLWH) continue to face a significantly elevated risk of chronic inflammation and Serious Non-AIDS Events (SNAEs). In this narrative review, we bridge the critical gap between molecular virology, immunometabolism, and clinical pathology by examining the complex interface of intrinsic immunity and viral persistence. We analyzed the evolutionary "arms race" between conserved host restriction factors, including TRIM5α, APOBEC3G, SAMHD1, BST-2, MX2, and SERINC, and the sophisticated viral evasion mechanisms that facilitate reservoir establishment. We further examined the role of bacterial translocation and gut barrier dysfunction in perpetuating systemic inflammation, emphasizing how HIV-1-mediated depletion of mucosal Th17 cells and disruption of tight junction proteins create a "leaky gut" that permits microbial product translocation despite suppressive therapy. Among viral proteins that may contribute to residual pathology during suppressive cART, we focused on the HIV-1 matrix protein p17, which has been proposed to function as a secreted "viral cytokine" from latent reservoirs, acting through CXCR1/CXCR2 receptors and the RACK1-JAK1-STAT1 pathway. Although primarily characterized in in vitro and ex vivo models, emerging data suggested that p17 may sustain systemic immune activation and metabolic reprogramming; however, its relative contribution compared with other viral proteins (Tat, Nef, gp120) in virologically suppressed patients remains to be fully delineated in human studies. Furthermore, we examined how HIV-1 hijacks cellular bioenergetics by shifting host cells from oxidative phosphorylation to aerobic glycolysis. We present an integrative model that connects restriction factor biology, p17-mediated chronic inflammation, immunometabolic dysregulation, and gut barrier dysfunction into a unified pathogenic framework, distinguishing established mechanisms from working hypotheses. Last, we assessed emerging therapeutic strategies, including CRISPR/Cas9-mediated enhancement of restriction factors, modulation of the mTOR pathway, and novel "Shock and Kill" approaches, stratified by development stage and demonstrated endpoints, offering potential pathways toward a functional cure.

Biowaste and agro-industrial co-products continue to increase with population growth and rising living standards, calling for scalable valorization strategies that go beyond simple mineralization. The black soldier fly (BSF) has emerged as a practical bioconversion platform capable of channeling biodegradable organic waste into high-value proteins, lipids, and chitin. In parallel, microbial interventions are increasingly recognized as key levers for substrate conditioning, process stabilization, and performance optimization in BSF-based systems. In this review, we adopted a function-first perspective to examine how microbial processes shape and connect three major biological valorization routes: aerobic composting, anaerobic digestion (AD), and BSF bioconversion. Rather than focus on taxonomic inventories, we synthesized evidence on microbial functions that matter in practice, including extracellular hydrolysis of complex polymers, regulation of short-chain fatty acids, detoxification and pathogen suppression, and process stabilization. We further reviewed microbe-assisted strategies, such as lactic pre-fermentation, directed acidogenesis, and probiotic or defined consortia and their effects on waste reduction, conversion efficiency, product quality, and sanitary safety. Finally, we translated these microbial mechanisms into scalable design principles for configuring and operating integrated insect–microbe systems, highlighting how microbial functions underpin reproducible, enterprise-ready performance across composting, AD, and BSF-integrated workflows.

Aquaculture expansion is occurring under accelerating climatic pressure. Warming, marine heatwaves, deoxygenation, salinity fluctuation, and intensified nutrient loading act simultaneously in aquaculture sediments, altering redox gradients and substrate fluxes that structure microbial communities. These stressors strengthen deterministic environmental filtering, reorganize interaction networks toward reduced-state dominance, and redistribute functional investment within sediment microbiomes; the biogeochemical engines regulating nutrient cycling, water quality, and disease dynamics. Such restructuring is associated with altered nitrogen processing, modified greenhouse gas fluxes, sulfide accumulation, enhanced pathogen performance, and enrichment of antimicrobial resistance determinants, with direct implications for production stability and disease risk. Evidence is synthesized to integrate quantified environmental forcing, ecological assembly mechanisms, and molecular functional responses into a unified framework linking microbial restructuring to ecosystem performance and operational resilience. Structural and functional microbial indicators suitable for early detection of redox compression and functional destabilization are evaluated, alongside resilience-oriented strategies spanning ecological design, microbiome management, engineering control, and adaptive monitoring. Despite substantial empirical progress, major gaps remain in resolving compound-stressor interactions, temporal reversibility, cross-system threshold comparability, and predictive modeling of microbial assembly under multi-driver forcing. Addressing these gaps is essential for developing mechanistically grounded, climate-resilient aquaculture systems.