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.
Through multi-omics integration, multi-omics approaches 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.
Combining improved feeding strategies, knowledge of gut microorganisms, biological analysis, and automated production could help produce insects with more predictable nutritional properties and 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
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.
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, De-Qi 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