Precision Nutrigenomics in Cultured Finfish: Dietary Regulation of Gene Expression, Microbial Ecology, Metabolism, and Immunity

Gut Microbiome of Aquatic Organisms: Role in Immunity Formation and Effects on Aquaculture Productivity

Aquaculture is central to global food security, but intensification of production has increased disease risk and environmental pressure. The gut microbiome of aquatic organisms is now recognized as a key mediator of host physiology, nutrition, immunity, and pathogen resistance, making it a promising alternative to antimicrobial-based disease control. This review summarizes current knowledge on the composition, assembly, and functional roles of the gut microbiome in fish and crustaceans of aquacultural importance. Major bacterial phyla include Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Actinobacteria, and Verrucomicrobia. Community structure is shaped by environment, diet, host age, genetics, stress, and stochastic processes, with differences between marine and freshwater systems. The microbiome contributes to immune defense through short-chain fatty acid production, Toll-like receptor signaling, cytokine regulation, mucosal immunoglobulin responses, antimicrobial peptide and bacteriocin production, and competitive exclusion of pathogens. It also supports productivity by improving nutrient assimilation, vitamin and enzyme synthesis, and feed conversion. Probiotics, prebiotics, and synbiotics are discussed as strategies for targeted microbiome modulation, although unstable colonization and the lack of standardized protocols remain major challenges. Overall, targeted microbiome manipulation offers a promising route toward sustainable, antimicrobial-reduced aquaculture.

Microbiota, fermentation, and metabolite biotransformation: Pathways to functional foods and personalised nutrition.

Dietary Regulation of Intestinal Stem Cell Function: Nutrient-Sensing, Microbiota-Mediated, and Regenerative Mechanisms from a Dietetic Perspective

The intestinal epithelium is a dynamic tissue renewed by intestinal stem cells (ISCs) within the crypt niche. ISC behavior is regulated not only by intrinsic genetic programs but also by dietary composition, nutrient availability, microbial metabolites, and feeding rhythms. This narrative review synthesizes mechanisms through which diet influences ISC self-renewal, proliferation, differentiation, metabolic programming, and regenerative capacity. Dietary patterns exert context-dependent effects: caloric restriction, fasting, and structured feeding–fasting cycles may enhance epithelial regeneration through nutrient-sensing pathways, mitochondrial adaptation, and circadian regulation, whereas Western-type and high-fat diets may promote niche remodeling, inflammation, metabolic reprogramming, and tumorigenic risk. Macronutrients regulate ISC fate through carbohydrate metabolism, amino acid sensing, fatty acid oxidation, and lipid-derived signaling molecules. Micronutrients, including vitamins A, D, and B and minerals such as iron, zinc, selenium, and magnesium, contribute to epithelial differentiation, redox balance, and barrier integrity. Phytochemicals may modulate ISC function through Wnt/β-catenin, Nrf2, SIRT1, and epigenetic pathways or by stabilizing the epithelial microenvironment. The gut microbiota mediates diet–ISC interactions via short-chain fatty acids, bile acids, indole derivatives, and other metabolites. However, human evidence remains limited, and studies integrating human organoids, single-cell analyses, metabolomics, and chrononutrition are needed to inform personalized nutritional strategies for intestinal health.

Role of Microbiome Manipulation in Enhancing Ruminant Digestion and Productivity: A Review

The rumen microbiome is a diverse and dynamic consortium of bacteria, archaea, protozoa, fungi, and viruses that supports feed degradation, nutrient transformation, animal health, and productive performance in ruminants. Advances in microbial ecology, sequencing technologies, and systems biology have created opportunities to manage this microbial ecosystem to improve the efficiency and sustainability of livestock production. This review examines the composition, functions, and ecological interactions of the rumen microbiome, with emphasis on its contribution to fibre digestion, volatile fatty acid production, microbial protein synthesis, feed conversion efficiency, methane formation, and host physiological functions. Current strategies for microbiome modulation, including dietary modification, probiotics, direct-fed microbials, prebiotics, synbiotics, phytogenic compounds, exogenous enzymes, and rumen microbial transplantation, are evaluated in relation to digestive efficiency and animal performance. Emerging approaches, including metagenomics, metatranscriptomics, metabolomics, precision nutrition, synthetic microbial communities, genome-editing tools, and artificial intelligence-based predictive models, are also considered as developing pathways for targeted microbiome engineering. These approaches may support improved nutrient utilisation, milk and meat production, animal health, and mitigation of greenhouse gas emissions from ruminant systems. However, practical implementation remains constrained by microbial ecosystem complexity, inter-animal variability, limited persistence of introduced microorganisms, economic considerations, and regulatory challenges. The review highlights the need to integrate multi-omics datasets, computational modelling, and precision livestock technologies to develop robust, scalable, and economically viable microbiome management strategies. A deeper understanding of host-microbiome interactions and microbial functional dynamics remains essential for translating scientific advances into practical approaches that support sustainable livestock production, environmental stewardship, and overall global food security.

Duckweed as a Novel Functional Food—Implications for Gut Microbiota Modulation

The gastrointestinal microbiota has a pivotal role in human health, orchestrating metabolic homeostasis, immunological activity, and nutrient bioavailability. Dietary modulation of gut microbiota is the simplest and most effective approach to preventing and managing metabolic and inflammatory disorders. Duckweed, particularly Wolffia species, has recently emerged as a sustainable, nutrient‐dense functional food with potential microbiome‐mediated benefits. Beyond its high‐quality protein content, duckweed provides fermentable fibers, polyphenols, minerals, and micronutrients including vitamin B 12 —that potentially influence gut microbial composition and metabolic activity. Evidence from compositional analyses, in vitro human colonic fermentation models, animal studies, and controlled dietary interventions suggests that duckweed‐derived substrates support short‐chain fatty acid production, generate bioactive phenolic metabolites, and interact with probiotic taxa, positioning duckweed as a prebiotic‐like matrix with synbiotic potential. Clinical studies within whole‐diet frameworks, such as green‐Mediterranean dietary patterns incorporating Wolffia globosa , report favorable metabolic outcomes alongside microbiome‐associated signals. This review synthesizes mechanistic, preclinical, and clinical evidence to reframe duckweed not just as another alternative protein, but as a microbiota‐accessible, synbiotic‐ready food matrix, while identifying the critical evidence gaps that currently limit clinical translation and regulatory constraints.

Health and Environmental Implications of Alternative Proteins in Human Diets: Nutritional Value, Gut Microbiota Modulation, and Sustainability Perspectives

Overall, alternative proteins represent a promising pathway toward sustainable food system transformation, but their successful integration will depend on evidence-based development, improved processing strategies, standardized evaluation, and supportive policy frameworks.