Jul 2026· Frontiers in Fish Science· 0 citations· 106 references
TL;DR
Despite the challenges in standardization, cost, and large-scale validation, advances in artificial intelligence, portable analytics, and open access omics data bases are accelerating the translation of these technologies into practical feed innovation.
Abstract
The rapid expansion of aquaculture and the ongoing transition from marine derived feed ingredients have intensified the need for precise tools to evaluate alternative diet formulations. Traditional compositional analyses are increasingly insufficient for this purpose, as they lack the potential to capture molecular complexity of novel plant-based, insect based and single cell protein ingredients. High-throughput omics technologies like metabolomics, proteomics, transcriptomics, metagenomics, and epigenomics are filling the gaps by characterization of molecular interactions, including identification of bioactive phytochemicals, anti-nutritional factors, and quality markers. Then they are integrated with dynamic
in-vitro
gastrointestinal simulations systems, multi-omics data can support rational pre-selection of experimental functional feeds before animal trails, reducing cost and ethical burden.
In vivo
validation through controlled feeding trials, integrated with multi-omics analyses, then allows mechanistic elucidation of host-diet-microbiome interactions and systematic biomarkers discovery for feed efficiency assessment. Nutriepigenomics adds further dimensions by how early nutritional programming induces lasting epigenetics modifications in fish, with implications for long term diet assessment. Throughout, the extraordinary physiological diversity of teleosts in trophic strategy, gut morphology, and genomic resources imposes meaningful constraints on cross-species data interpretation that the field must acknowledge rigorously. Despite the challenges in standardization, cost, and large-scale validation, advances in artificial intelligence, portable analytics, and open access omics data bases are accelerating the translation of these technologies into practical feed innovation.
This review evaluates multi-omics applications in dairy research across nutrition, safety, and health. Through multi-omics integration, we reveal nutrient differences driven by species, rearing practices, and processing techniques, identify protein patterns and allergen profiles, and construct adulteration detection fingerprints and species-specific peptide markers, thereby improving the timeliness and accuracy of safety assessment. The coupling of metagenomics and metabolomics effectively predicts spoilage-related microbial risks, enabling better risk control. Furthermore, multi-omics approaches systematically elucidate the functional mechanisms of bioactive peptides (e.g., ACE-inhibitory peptides), clarify the prebiotic effects of functional oligosaccharides, and build interaction networks between dairy components and gut microbiota. The introduction of machine learning enables origin and shelf-life prediction, as well as the discovery of novel biomarkers, promoting personalized nutrition and precision fermentation strategies. However, the field is currently constrained by severe reproducibility issues arising from the absence of standardized operating procedures, excessive optimism regarding machine learning models that rarely generalize across laboratories or product matrices, and a persistent disconnect between laboratory-scale biomarker discovery and industrial implementation. Without rigorous cross-platform validation and openly shared multi-omics reference datasets, most published markers remain unfit for regulatory or industrial application. Future efforts should establish standardized workflows and expand the evidence base to drive the dairy industry toward safer, healthier, and more traceable directions.
Simple Summary The growing demand for sustainable sources of food and animal feed has increased interest in edible insects, which can convert low-value organic materials into nutritious biomass. However, their nutritional composition can vary depending on what they eat and how they are reared, making it difficult to consistently produce insects with desired nutritional properties. This review examines how diet and the communities of microorganisms living in the insect gut work together to influence growth, nutrient use, fats, proteins, and other valuable compounds. The available evidence shows that diets containing agricultural by-products, food residues, seaweeds, and other nutrient-rich materials can change the nutritional composition and quality of edible insects. The review also shows that gut microorganisms contribute to digestion, nutrient transformation, adaptation to different diets, and the conversion of organic materials into useful biomass. However, important gaps remain because the mechanisms behind these interactions are not yet fully understood and production methods are not sufficiently standardized. Combining improved feeding strategies, knowledge of gut microorganisms, biological analysis, and automated production could help produce insects with more predictable nutritional properties. This approach could support sustainable food and feed production, reduce organic waste, and strengthen circular and resource-efficient agricultural systems.
M. Ezzaitouni, Tarik Chileh Chelh, E. Belarbi et al.· Insects· 0 citations
BackgroundWhile global nutrition policies increasingly promote plant-based diets for environmental sustainability, this approach may implicitly assume biological homogeneity and overlook interindividual genetic variability in nutrient metabolism.AimThis review evaluates potential molecular bottlenecks and genetic variations that may influence individual adaptation to plant-based dietary patterns, based on recent literature in nutrigenetics and micronutrient metabolism.MethodsPeer-reviewed literature published primarily between 2015 and 2025 was searched across PubMed, Web of Science, and Scopus using nutrigenetics- and plant-based nutrition-related terms; Google Scholar was additionally consulted for supplementary citation tracking. Foundational studies were included where mechanistically relevant. Studies lacking genotypic data, in vitro models without clinical relevance, and non-English publications were excluded.SummaryCurrent evidence suggests that the conversion efficiency of plant-derived precursors into biologically active forms differs according to polymorphisms in genes including fatty acid desaturases (FADS1/FADS2), beta-carotene oxygenase-1 (BCO1), and phosphatidylethanolamine N-methyltransferase (PEMT). Moreover, phytate-mediated constraints and variations affecting mineral absorption-transmembrane serine protease 6 (TMPRSS6) and solute carrier family 39 member 4 (SLC39A4)-and vitamin B12 transport-fucosyltransferase-2 (FUT2) and transcobalamin-2 (TCN2)-may increase susceptibility to subclinical micronutrient insufficiencies in genetically predisposed individuals. Although many associations reach statistical significance, their clinical impact varies across populations and depends on the overall dietary context. These genetic influences are not deterministic and may potentially be mitigated through targeted dietary planning and personalized supplementation. Precision nutrition frameworks incorporating genetic variability may improve dietary personalization; however, future large-scale longitudinal trials are required before these findings can address consensus clinical guidelines.
Eren Terzioğlu, Indrani Kalkan· Nutrition and Health· 0 citations
Precision nutrigenomics requires a diet–microbiome–host perspective because microorganisms can transform feed substrates, generate bioactive metabolites, compete with pathogens, and modify intestinal and systemic gene regulation. This structured narrative review synthesizes representative controlled feeding trials, transcriptomic and targeted gene-expression studies, microbiome analyses, and complementary multi-omic evidence concerning dietary regulations in cultured finfish. The available evidence is concentrated particularly on soybean-derived proteins, lipid-source replacements, selected amino acids and micronutrients, functional additives, probiotics, and fermented ingredients in a limited range of cultured finfish species; therefore, the synthesis is not intended to provide exhaustive coverage of every dietary intervention or finfish taxon. Recurrent host responses involve intestinal inflammation and barrier integrity, nutrient transport, lipid and bile-acid metabolism, long-chain polyunsaturated fatty-acid biosynthesis, targets of rapamycin/insulin-like growth factor (TOR/IGF) signaling, and nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) antioxidant defense. The expanded microorganism-centered synthesis shows that dietary effects depend on microbial niche, substrate availability, community succession, metabolite production, and strain-specific probiotic or pathobiont activity. Lactic-acid bacteria, Bacillus-associated interventions, butyrate-generating strategies, fermented ingredients, and microbial biomass may support digestion, immune balance, and disease resistance, but taxonomic shifts alone do not demonstrate functional benefit. Current evidence is limited by extensive reliance on 16S ribosomal RNA (16S rRNA) relative-abundance data, inconsistent digesta-versus-mucosa sampling, inadequate feed and water controls, and weak causal validation. Future precision aquafeed studies should combine host transcriptomics with absolute microbial quantification, shotgun metagenomics, metatranscriptomics, metabolomics, culturomics, histology, and pathogen challenge. Integrating microbial function with host phenotype can improve sustainable feed design, intestinal health, and resilience.
Md. Hashibur Rahman, Hyuncheol Jeon, Haham Kim et al.· Microorganisms· 0 citations
This review outlines foundational applications of omics in aquaculture and highlights the characteristics and current applications of distinct omics approaches, and summarizes three core application domains of omics in aquaculture.
Chao Guo, Deqi Sun, Ben Yang et al.· Fishes· 0 citations
BACKGROUND
The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience.
RESULTS
We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA p > 0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. Bacteroides fragilis emerged as a dominant associate, correlating positively with a diverse range of metabolites (n = 271). Functional gene analysis suggested a link between Mediterraneibacter spp. and soyasaponin deglycosylation, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps.
CONCLUSION
Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.
G. Pangga, A. Richmond, C. Hughes et al.· Animal Microbiome· 0 citations