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Keywords = gene–diet interaction

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43 pages, 15802 KB  
Review
Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk
by Zhongquan Jiang, Jiale Chen, Yuanhao Ren, Tingting Lin, Siping Li, Fengyuan Shen, Bo Qin, Lei Li, Changjian Li, Na Ying and Hanfeng Zheng
Biology 2026, 15(13), 1066; https://doi.org/10.3390/biology15131066 - 3 Jul 2026
Viewed by 246
Abstract
The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based [...] Read more.
The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome–mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater–seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG–MGE associations. Risk assessment should therefore move beyond ARG abundance toward host–ARG–MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons. Full article
(This article belongs to the Special Issue Intestinal Health of Aquatic Animals)
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16 pages, 1950 KB  
Article
Integrated Inflammatory and Gut Microbial Signatures in Major Depressive Disorder: A Case–Control Study
by Nour Dabboussi, Espérance Debs, Marc Bouji, Raymond Kassab, Rami Bou Khalil, Nassim Fares and Rayane Rafei
Brain Sci. 2026, 16(7), 681; https://doi.org/10.3390/brainsci16070681 - 28 Jun 2026
Viewed by 218
Abstract
Background/Objectives: Major depressive disorder (MDD) is increasingly recognized as involving inflammation and the microbiota–gut–brain axis. Few studies have simultaneously assessed systemic inflammatory markers and gut microbiota composition within the same cohort while accounting for metabolic confounders. Moreover, data from Middle Eastern and North [...] Read more.
Background/Objectives: Major depressive disorder (MDD) is increasingly recognized as involving inflammation and the microbiota–gut–brain axis. Few studies have simultaneously assessed systemic inflammatory markers and gut microbiota composition within the same cohort while accounting for metabolic confounders. Moreover, data from Middle Eastern and North African (MENA) populations remain limited, restricting our understanding of how diet may influence neuroimmune–microbiome interactions in depression. This study aimed to investigate associations between MDD, systemic inflammatory markers, and gut microbiota composition in Lebanese adults. To our knowledge, this is the first study of its kind in Lebanon, as well as in the MENA region. Methods: In this cross-sectional case–control study, we examined circulating inflammatory markers and gut microbial profiles in 46 adults with DSM-5-confirmed MDD and 25 healthy controls. Plasma C-reactive protein (CRP) and interleukin-6 (IL-6) were measured, and the gut microbiota composition was characterized using 16S rRNA gene sequencing. Multivariable models were adjusted for age, sex, body mass index (BMI), Mediterranean diet adherence, and fluoxetine exposure. Results: Depression status was not independently associated with CRP or IL-6 after adjustment, whereas BMI emerged as a significant determinant of systemic inflammation. At the genus level, MDD was associated with the enrichment of Dorea, Lachnoclostridium, Collinsella, Bilophila, and Klebsiella and the depletion of Christensenella, Mitsuokella, and Victivallis, independent of inflammatory biomarkers. Alpha diversity did not differ between groups, while beta diversity showed modest metric-dependent differences, primarily driven by presence/absence-based measures. Conclusions: Specific microbial taxa may contribute to gut–brain signaling pathways implicated in MDD and systemic inflammation. Further longitudinal and mechanistic studies are required to clarify causal interactions within inflammation–microbiome networks in MDD. Full article
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20 pages, 19634 KB  
Article
AI-Integrated Multi-Target Validation of Coreopsis tinctoria Polyphenols as a Functional Food Ingredient Against Diabetic Nephropathy
by Dilinare Abdurehman, Xueying Lu, Yindengzhi Guoruoluo, Geyu Liu, Jun Li, Tao Wu, Xuelei Xin and Haji Akber Aisa
Foods 2026, 15(13), 2257; https://doi.org/10.3390/foods15132257 - 23 Jun 2026
Viewed by 246
Abstract
Diabetic nephropathy (DN) is a severe diabetic complication with substantial clinical burden. The complex pathogenesis of DN has hindered the development of targeted therapies, creating an urgent need to develop novel strategies that directly address its underlying inflammatory and fibrotic mechanisms. Coreopsis tinctoria [...] Read more.
Diabetic nephropathy (DN) is a severe diabetic complication with substantial clinical burden. The complex pathogenesis of DN has hindered the development of targeted therapies, creating an urgent need to develop novel strategies that directly address its underlying inflammatory and fibrotic mechanisms. Coreopsis tinctoria (CE) is an edible plant rich in polyphenols, but its mechanism against DN remains understood. An integrated framework combining network pharmacology and machine learning was developed to prioritize active polyphenols and their targets. A multi-layer perceptron classifier, trained on 3.16 million compound–target pairs from Binding DB, predicted interactions between 36 CE polyphenols and 12,030 DN-associated genes. The top 100 targets were subjected to KEGG enrichment analysis, and the identified pathways were validated in a high-fat diet/STZ-induced DN rat model. The MLP model achieved superior performance (AUC-ROC = 0.9219, AP = 0.9592). Five lead polyphenols (flavonoids/chalcones) showed high predicted activity. KEGG analysis revealed enrichment in PI3K-Akt, calcium signaling, metabolic pathways, and cellular senescence. In vivo, CE treatment (150–600 mg/kg/day) dose-dependently improved glucose/lipid metabolism and renal function, and ameliorated histopathological damage, including glomerular hypertrophy, fibrosis, and mesangial expansion. Mechanistically, CE suppressed NFκB/TGFβ/Smad signaling, restored PPARγ and Nrf2/HO-1/FoxO1 antioxidant defenses, and inhibited apoptosis via Bcl-2/Bax regulation. CE exerts multi-target renoprotective effects through coordinated modulation of metabolic, inflammatory, fibrotic, and antioxidant pathways, supporting its potential as a functional food ingredient for DN management. Full article
(This article belongs to the Section Food Nutrition)
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16 pages, 8143 KB  
Article
Pseudostellaria heterophylla Extract Enhances the Immune Responses in Larimichthys crocea Against Pseudomonas plecoglossicida Infection
by Kun Huang Han, Zi Min Li, Li Zhou, Dong Ling Zhang, Ying Li, Zhao Han Sun, Jia Chen, Zhi Deng Lin, Yan Bin Dai and Peng Fei Zou
Fishes 2026, 11(6), 371; https://doi.org/10.3390/fishes11060371 - 22 Jun 2026
Viewed by 228
Abstract
Visceral white spot disease caused by Pseudomonas plecoglossicida poses a severe threat to large yellow croaker (Larimichthys crocea) aquaculture. This study investigated the immunomodulatory effects and underlying mechanisms of Pseudostellaria heterophylla extract against P. plecoglossicida infection in L. crocea. Fish [...] Read more.
Visceral white spot disease caused by Pseudomonas plecoglossicida poses a severe threat to large yellow croaker (Larimichthys crocea) aquaculture. This study investigated the immunomodulatory effects and underlying mechanisms of Pseudostellaria heterophylla extract against P. plecoglossicida infection in L. crocea. Fish were fed a basal diet supplemented with 1% P. heterophylla extract for 30, 45, and 60 days, followed by intraperitoneal injection with 200 μL P. plecoglossicida (1 × 104 CFU/mL). When the control group reached about 50% mortality, transcriptome sequencing of head kidney tissues was performed on the 45 and 60 days post-feeding of the treatment groups to analyze gene expression changes following bacterial infection. Survival rates of the treatment groups were 33.33%, 13.33%, and 20% higher than those of the control group at 30, 45, and 60 days post-feeding, respectively. Transcriptomic analysis revealed time-dependent transcriptional responses: in one group, 45 days post-feeding, 10 differentially expressed genes (DEGs) were identified (2 up-regulated and 8 down-regulated), whereas in another group, 60 days post-feeding, 893 DEGs were detected (417 up-regulated and 476 down-regulated). Functional enrichment analysis (GO, KEGG, and GSEA) demonstrated that DEGs were significantly enriched in immune-related pathways, including Toll-like receptor signaling, chemokine activity, Th1 and Th2 cell differentiation, hematopoietic cell lineage, and cytokine–cytokine receptor interaction. Key immune genes, including chemokines, Toll-like receptors, and T cell regulators, were significantly up-regulated. These findings indicate that P. heterophylla extract enhances both the specific and non-specific immune capabilities of L. crocea in a time-dependent manner, with prolonged supplementation eliciting more robust transcriptional activation of immune defense pathways. This study provides a scientific foundation for developing immunological prevention strategies against P. plecoglossicida infection in aquaculture. Full article
(This article belongs to the Special Issue Recent Studies on Pathogen-Host Interaction of Aquatic Animals)
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15 pages, 1007 KB  
Article
Effects of Dietary Standardized Ileal Digestible Lysine and Amylose/Amylopectin Ratio on Intestinal Morphology, Barrier-Related Gene Expression, and Cecal Microbiota in Broilers Fed Low-Protein Diets
by Minhao Zhang and Jianmin Yuan
Animals 2026, 16(12), 1914; https://doi.org/10.3390/ani16121914 - 20 Jun 2026
Viewed by 280
Abstract
This study investigated the effects of dietary standardized ileal digestible (SID) lysine levels and amylose to amylopectin ratios on the intestinal health of broilers fed an 18.5% crude protein diet from 22 to 42 days of age. A total of 540 healthy male [...] Read more.
This study investigated the effects of dietary standardized ileal digestible (SID) lysine levels and amylose to amylopectin ratios on the intestinal health of broilers fed an 18.5% crude protein diet from 22 to 42 days of age. A total of 540 healthy male Ross 308 broilers were randomly assigned to nine treatments in a 3 × 3 factorial design consisting of three SID lysine levels (1.00%, 1.20%, and 1.40%) and three AM/AP ratios (0.19, 0.29, and 0.41), with six replicates of 10 birds each. Ileal morphology, intestinal barrier function and inflammation-related gene expression, and the composition of cecal microbiota were evaluated. Significant interactions between lysine level and AM/AP ratio were observed for Occludin, ZO-1, Claudin-1, and TNF-α expression, with the highest expression in the 1.40% lysine + 0.41 AM/AP group and the lowest in the 1.00% lysine + 0.19 AM/AP group. The VH/CD ratio showed a significant interaction, with the highest value in the 1.20% lysine + 0.19 AM/AP group and the lowest in the 1.40% lysine + 0.41 AM/AP group. IL-18 and IL-10 were primarily affected by the main effects of lysine and AM/AP ratio. The expression levels of both IL-10 and IL-18 increased with increasing lysine level and increasing starch AM/AP ratio. Dietary SID lysine level and AM/AP ratio interactively regulate the expression of barrier-related genes, inflammatory status, intestinal morphology, and cecal microbiota, potentially contributing to enhanced intestinal health in broilers. However, because microbial metabolites were not measured, the functional significance of the observed microbiota alterations remains speculative. In broilers fed an 18.5% CP diet, a combination of 1.20% SID lysine with an AM/AP ratio of 0.19 was identified as the optimal strategy for maintaining intestinal morphology from 22 to 42 days of age. Full article
(This article belongs to the Section Poultry)
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25 pages, 4998 KB  
Article
Maternal Rumen-Protected Leucine Supplementation Enhances Placental Nutrient Transport Capacity and Increases Birth Weight in Hu Sheep
by Qin Gao, Chong Yuan, Shanglai Li, Hua Yang, Zongyou Wei and Yanli Zhang
Vet. Sci. 2026, 13(6), 592; https://doi.org/10.3390/vetsci13060592 - 18 Jun 2026
Viewed by 311
Abstract
Leucine, an essential branched-chain amino acid, serves not only as a substrate for protein synthesis but also as a key regulator of placental function and fetal development. This study investigated the effects of dietary supplementation with RP-Leu during late gestation on placental development [...] Read more.
Leucine, an essential branched-chain amino acid, serves not only as a substrate for protein synthesis but also as a key regulator of placental function and fetal development. This study investigated the effects of dietary supplementation with RP-Leu during late gestation on placental development and offspring performance in Hu sheep. Sixty twin-pregnant ewes at day 80 of pregnancy were randomly assigned to either a control group (fed a basal diet) or an RP-Leu group (fed a basal diet supplemented with 19 g/day RP-Leu). The feeding trial lasted for 60 d. The ewes were slaughtered at day 140 of gestation. Maternal slaughter traits and fetal organ weights were recorded. Blood and milk samples were collected for milk composition analysis and targeted metabolomic profiling. Leucine supplementation significantly increased the percentage of milk fat content, total solid content, and the birth weight of lambs (p < 0.05). Improvements in placental morphology and antioxidant capacity were observed, including a significant increase in cotyledon density and a significant enhancement of catalase (CAT) activity (p < 0.05). Gene expression analysis indicated that the NOS3, SLC38A1 and FABP4 genes in the placental cotyledons (p < 0.05), and the VEGFA, NOS3, SLC27A1 and FABP4 genes were significantly upregulated in the maternal caruncles (p < 0.05). Plasma metabolomic profiling revealed increased L-glutamic acid levels and alterations in several amino acids, with pathway enrichment indicating involvement in amino acid metabolism and membrane transport processes. Transcriptomic analysis identified 739 differentially expressed genes, which were mainly enriched in the PI3K/Akt signaling pathway, ECM–receptor interaction pathway, and cytokine–cytokine receptor interaction pathway. Collectively, these findings suggest that RP-Leu supplementation during late gestation may enhance offspring growth by modulating amino acid metabolism, promoting placental development, and improving placental nutrient transport capacity, thereby supporting fetal growth and development. Full article
(This article belongs to the Special Issue Advances in Veterinary Theriogenology: Reproduction and Fertility)
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18 pages, 1537 KB  
Article
Dietary Guanidinoacetic Acid Improves Meat Tenderness and Antioxidant Capacity in Rabbits via Modulating Muscle Fiber Characteristics and Fat Metabolism
by Yanhui Liang, Xi Chen, Xiaoyu Fan, Yingmei Zhang, Shengnan Wang, Xiaojia Wu, Yingle Wei, Changmao Wei, Yichen Lin, Qinghua Liu and Changchuan Ye
Animals 2026, 16(12), 1827; https://doi.org/10.3390/ani16121827 - 12 Jun 2026
Viewed by 240
Abstract
As the direct biosynthetic precursor of creatine, guanidinoacetic acid (GAA) exerts a pivotal regulatory role in energy homeostasis and protein metabolism. Rabbit meat has garnered increasing global recognition as a healthy food source, characterized by its outstanding high-protein and low-fat nutritional profile. Accordingly, [...] Read more.
As the direct biosynthetic precursor of creatine, guanidinoacetic acid (GAA) exerts a pivotal regulatory role in energy homeostasis and protein metabolism. Rabbit meat has garnered increasing global recognition as a healthy food source, characterized by its outstanding high-protein and low-fat nutritional profile. Accordingly, the optimization of rabbit meat quality has attracted growing attention from both consumers and animal production practitioners. In the present study, we evaluated the impacts of dietary GAA supplementation on meat quality traits, in vivo antioxidant capacity, muscle fiber characteristics, and fatty acid metabolism in New Zealand white rabbits. A total of 960 male New Zealand white rabbits were assigned to two age groups: 40-day-old group and 60-day-old group (40 ± 2 days, 1.19 ± 0.09 kg; 60 ± 2 days, 1.82 ± 0.15 kg). Within each age group, rabbits were randomly allocated to a control diet or a diet supplemented with 100 mg/kg GAA (CON-40, GAA-40, CON-60, GAA-60). After a 45-day feeding period, two-way ANOVA revealed that GAA supplementation significantly reduced shear force (p < 0.01, diet main effect) and muscle fiber density (p < 0.01, diet main effect), with an age-dependent effect on shear force (age × diet interaction, p < 0.05). Moreover, GAA enhanced systemic antioxidant capacity, as indicated by increased serum superoxide dismutase (SOD) activity (p < 0.01) and total antioxidant capacity (T-AOC) (p < 0.05), while no significant effect on malondialdehyde (MDA) was detected under the current experimental conditions. GAA also regulated the expression of lipid metabolism-related genes (FAS, HSL, ACC) in intramuscular and perirenal fat, indicating its regulatory effect on fatty acid metabolism. In conclusion, dietary GAA supplementation improves rabbit meat tenderness and antioxidant capacity, with no negative effects on growth performance. These findings confirm that GAA has the potential to serve as a nutritional strategy to improve rabbit meat quality, supporting the development of rabbit meat as a functional food for human consumption. Full article
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26 pages, 8195 KB  
Review
A Chrono-Metabolic Approach to Mental Health: Current Perspectives on Circadian Rhythms, Gut Microbiota, and Microbial Metabolites in Mood Disorders
by Giuseppe Marano, Mariateresa Acanfora, Luca Conci, Gianandrea Traversi, Osvaldo Mazza, Esmeralda Capristo, Eleonora Gaetani, Gianluca Franceschini and Marianna Mazza
Metabolites 2026, 16(6), 400; https://doi.org/10.3390/metabo16060400 - 9 Jun 2026
Viewed by 498
Abstract
Growing evidence indicates that the gut microbiota is not a static ecosystem but a rhythmic metabolic organ whose oscillatory activity is tightly coordinated with host circadian biology. Disruption of this temporal alignment, through irregular diet, sleep disturbance, shift work, or social jet lag, [...] Read more.
Growing evidence indicates that the gut microbiota is not a static ecosystem but a rhythmic metabolic organ whose oscillatory activity is tightly coordinated with host circadian biology. Disruption of this temporal alignment, through irregular diet, sleep disturbance, shift work, or social jet lag, may profoundly alter microbial composition and the production of neuroactive metabolites. These alterations have emerged as potential contributors to the pathophysiology of mood disorders. This review introduces the concept of chrono-metabolic psychiatry, a framework integrating circadian rhythms, gut microbiota dynamics, and host metabolic signaling in the development and course of depressive and bipolar disorders. In this framework, the term “chrono-metabolic” refers to the integration of biological timing, host metabolic regulation, and microbiota-derived metabolic signaling. Chrono-metabolic psychiatry therefore shifts the focus from static dysbiosis or neurotransmitter imbalance alone to the time-dependent interactions among circadian misalignment, microbial rhythmicity, immune regulation, metabolite production, and affective instability. Diurnal fluctuations in short-chain fatty acids, tryptophan–kynurenine metabolites, bile acids, and microbial-derived neurotransmitters interact with clock gene regulation, hypothalamic–pituitary–adrenal axis activity, neuroinflammation, and synaptic plasticity. Chrono-disruption may represent a transdiagnostic vulnerability factor and may confirm the bidirectional relationship between mood instability and microbiota rhythmicity. Emerging therapeutic implications, including chrono-nutrition, time-restricted feeding, targeted probiotic administration (“chronobiotics”), and the microbiota-modulating effects of psychotropic medications are discussed. By shifting from a compositional to a temporal–metabolic perspective, this model highlights the importance of microbial oscillations rather than static dysbiosis alone. Integrating circadian biology into microbiota research may enable metabolomic stratification and pave the way for precision psychiatry approaches grounded in host–microbe metabolic crosstalk. Future longitudinal and time-resolved multi-omics studies are needed to validate this framework and to translate it into clinically actionable interventions. Full article
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17 pages, 2943 KB  
Article
Feeding All-Trans Retinoic Acid to Pregnant Sows Regulates the Development of the Pulmonary Nervous Systems of Neonatal Pigs
by Haimei Zhou, Xianghao Xiao, Wei Lu and Yuyong He
Vet. Sci. 2026, 13(6), 565; https://doi.org/10.3390/vetsci13060565 - 7 Jun 2026
Viewed by 372
Abstract
Newborn piglets in intensive pig farms are often prone to pulmonary diseases due to underdeveloped fetal lung neural systems, and ATRA is often regarded as an important morphogen that displays pleiotropic functions during embryonic development. However, information about the effect of maternal administration [...] Read more.
Newborn piglets in intensive pig farms are often prone to pulmonary diseases due to underdeveloped fetal lung neural systems, and ATRA is often regarded as an important morphogen that displays pleiotropic functions during embryonic development. However, information about the effect of maternal administration with ATRA on the peripheral neural system of fetal lungs is still scare. Fifteen pregnant sows were assigned to the ATRA0 (0 mg/kg diet), ATRA4, ATRA8, ATRA16 and ATRA32 treatment groups and offered their own feed from d12 to d95 after artificial insemination; then two neonatal pigs with birth weights similar to the average birth weight were taken out from each litter for the collection of lung samples, and samples were subjected to immunofluorescence staining, RNA-seq and RT-qPCR assays. Results indicated that compared to newborn piglets from the ATRA0 treatment group, newborn piglets from the ATRA4 treatment group had higher percentages of GFAP-positive astrocyte cells (p < 0.05) and GFAP-TUBB3 colocalization (p < 0.05) in the lungs. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that differential expressed genes are mainly enriched in the pathways of neuroactive ligand–receptor interaction, GABAergic synapses and cell adhesion molecules. Addition of ATRA at 4 mg/kg to the diet of pregnant sows can enhance the healthy development of the pulmonary nervous systems of fetal pigs. Full article
(This article belongs to the Special Issue Swine Nutrition and Feed)
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25 pages, 6816 KB  
Review
The Nutri-Exposome Intelligence Framework: Integrating Multi-Omics, Machine Learning, and Digital Nutrition for Precision Chronic Disease Prevention
by Mia Yang Ang and Siew Woh Choo
Nutrients 2026, 18(11), 1826; https://doi.org/10.3390/nu18111826 - 5 Jun 2026
Viewed by 747
Abstract
Background/Objectives: Precision nutrition is moving beyond population-based guidance and isolated gene–diet interactions toward integrative models of dietary response. However, current approaches remain fragmented across nutrigenomics, microbiome research, multi-omics profiling, digital health, and machine learning. This review proposes the Nutri-Exposome Intelligence Framework as a [...] Read more.
Background/Objectives: Precision nutrition is moving beyond population-based guidance and isolated gene–diet interactions toward integrative models of dietary response. However, current approaches remain fragmented across nutrigenomics, microbiome research, multi-omics profiling, digital health, and machine learning. This review proposes the Nutri-Exposome Intelligence Framework as a conceptual, data science-driven model for integrating cumulative dietary, environmental, microbial, molecular, clinical, and digital exposures for precision chronic disease prevention. Methods: This conceptual review synthesizes the literature on precision nutrition, nutrigenetics, nutrigenomics, exposomics, gut microbiome research, multi-omics integration, wearable and biomarker-based monitoring, and machine learning in nutrition studies. Evidence was organized into a framework linking exposure assessment, host susceptibility, microbiome-mediated biotransformation, molecular response profiling, computational modelling, personalized intervention, and longitudinal feedback. Results: The proposed framework consists of seven interconnected layers: diet, environment, and lifestyle exposures; host genome and microbiome; multi-omics molecular responses; machine learning-based integration; risk prediction and responder stratification; personalized dietary intervention; and wearable and biomarker-based feedback. It positions the nutri-exposome as a cumulative exposure–response system and highlights how machine learning can support data harmonization, feature engineering, predictive modelling, responder classification, explainable interpretation, and adaptive refinement of dietary recommendations. Key applications include obesity, type 2 diabetes, cardiovascular disease, metabolic dysfunction-associated steatotic liver disease, cardiovascular–kidney–metabolic syndrome, and broader cardiometabolic prevention. Conclusions: Nutri-exposome intelligence offers a structured pathway for transforming complex nutrition data into predictive, explainable, and adaptive precision nutrition strategies. Implementation will require longitudinal and multi-ethnic cohorts, standardized metadata, causal validation, interpretable machine learning, ethical governance, and equitable access to support responsible clinical and public health translation globally. Full article
(This article belongs to the Special Issue Data Science and Machine Learning for Nutrition Studies)
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14 pages, 256 KB  
Article
Beyond the FTO Gene: Environmental and Behavioural Factors Associated with BMI and Overweight in Spanish Adolescents
by Luciana Margara, Inés Piñas-Bonilla, Pablo Abián, Alfredo Bravo-Sánchez, David Ortiz-Sánchez, María Ramírez-delaCruz, Paula Esteban-García, Javier Portillo, Carlos Ramírez and Javier Abián-Vicén
Children 2026, 13(6), 782; https://doi.org/10.3390/children13060782 - 4 Jun 2026
Viewed by 363
Abstract
Background/objectives: Obesity is a multifactorial condition influenced by interactions between genetic susceptibility and environmental factors. The fat mass and obesity-associated (FTO) gene has been widely linked to obesity risk, particularly the rs9939609 polymorphism, which is associated with higher body mass index [...] Read more.
Background/objectives: Obesity is a multifactorial condition influenced by interactions between genetic susceptibility and environmental factors. The fat mass and obesity-associated (FTO) gene has been widely linked to obesity risk, particularly the rs9939609 polymorphism, which is associated with higher body mass index (BMI) and adiposity. However, evidence in adolescents remains inconsistent, and lifestyle factors such as physical activity and diet may modify genetic risk. The objectives of this study were: (i) to examine the influence of environmental, genetic, physical activity, and dietary factors on the BMI and overweight-related variables of adolescents, and (ii) to assess the impact of the rs9939609 polymorphism in the FTO gene on these variables. Methods: A cross-sectional study was conducted involving 206 adolescents aged 12 to 16 years. Body mass index (BMI), physical fitness, physical activity levels, adherence to the Mediterranean diet, mobile phone usage, and FTO rs9939609 genotyping from buccal swabs were collected. Results: No significant associations were found between the FTO genotype and BMI, or with physical activity, mobile phone usage and dietary habits. Boys showed higher physical fitness and physical activity levels than girls (p < 0.05). The only factor significantly associated with BMI was regular breakfast consumption: adolescents who habitually ate breakfast had a lower prevalence of overweight (χ2 = 7.98, p = 0.005). Conclusions: The rs9939609 polymorphism in the FTO gene was not associated with overweight in this adolescent cohort. The findings underscore the relevance of healthy behaviours, particularly regular breakfast consumption and physical activity, especially among boys, as factors potentially associated with lower prevalence of overweight during adolescence. Full article
22 pages, 2853 KB  
Review
One Diet Does Not Fit All: A Systematic Review and Meta-Analysis of Gene–Diet Interactions Affecting Blood Lipid Profiles
by Saba Iordanishvili, Nazibrola Chiradze, Dodo Agladze, Marine Kikvidze, Revaz Solomonia and Vincenzo Lagani
Curr. Issues Mol. Biol. 2026, 48(6), 591; https://doi.org/10.3390/cimb48060591 - 3 Jun 2026
Viewed by 323
Abstract
Blood lipid responses to diet vary substantially between individuals, limiting the effectiveness of uniform dietary recommendations, and genetic variation may contribute to this heterogeneity through gene–diet interactions. This systematic review and meta-analysis evaluated nutrigenetic interactions affecting blood lipid traits. Web of Science Core [...] Read more.
Blood lipid responses to diet vary substantially between individuals, limiting the effectiveness of uniform dietary recommendations, and genetic variation may contribute to this heterogeneity through gene–diet interactions. This systematic review and meta-analysis evaluated nutrigenetic interactions affecting blood lipid traits. Web of Science Core Collection and MEDLINE were searched in April 2026 to identify human studies testing interactions between dietary exposures—including macronutrient composition, fat quantity, fat type [polyunsaturated fatty acids (PUFA), monounsaturated fatty acids (MUFA), and saturated fatty acids (SFA)], carbohydrate, and protein—and lipid-related genes. Interaction p-values were synthesized using a weighted Stouffer’s Z method with Benjamini–Hochberg false discovery rate correction. Twenty studies (n = 20), comprising approximately 9800 participants, met the inclusion criteria. The most consistent evidence was observed for CETP, APOE, and APOB, particularly in relation to broader macronutrient composition and fat-related exposures, while ABCA1 and APOA5 showed significant but more limited evidence. PUFA was the most consistent specific dietary exposure. In contrast, ABCG5, ABCG8, and CYP7A1 lacked sufficient data for meta-analysis, highlighting major gaps in the current literature. Overall, the findings support the view that lipid responses to diet are partly genotype-dependent, while also underscoring the need for larger, better harmonized studies to clarify and extend the current evidence base. Full article
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21 pages, 5263 KB  
Article
Transcriptome and Metabolome Analyses Reveal the Molecular Relationship Between Dietary Crude Protein Level and Liver Metabolism in Fattening Hu Sheep
by Patiguli Abudukeyimu, Fengmei Xie, Yifan Hu, Haiying He, Cheng Hou, Yiming Sulaiman, Huiguo Yang and Gao Gong
Metabolites 2026, 16(6), 375; https://doi.org/10.3390/metabo16060375 - 29 May 2026
Viewed by 275
Abstract
Background: Dietary crude protein (CP) acts as a key nutritional factor that affects the growth performance and liver metabolism of fattening Hu sheep, with metabolizable energy (ME) representing a major confounding factor in CP-related responses. To isolate the specific effects of CP on [...] Read more.
Background: Dietary crude protein (CP) acts as a key nutritional factor that affects the growth performance and liver metabolism of fattening Hu sheep, with metabolizable energy (ME) representing a major confounding factor in CP-related responses. To isolate the specific effects of CP on liver metabolism and minimize energy–protein interactions, we standardized dietary ME at 9.4 MJ/kg dry matter. Methods: We then established three isoenergetic CP concentrations: 11.07%, 13.07%, and 15.11%. A total of ninety 4-month-old male Hu sheep (with an initial body weight of 27.09 ± 1.83 kg) were allocated at random to three dietary treatment groups, each containing 30 animals distributed across three replicate pens, and fed pelleted total mixed rations (PTMRs) for 75 days under pen conditions in southern Xinjiang. Exploratory combined transcriptomic and metabolomic profiling of liver tissue was conducted to characterize how graded CP levels modulate growth traits and hepatic metabolic pathways, thereby identifying the appropriate dietary CP level for efficient and sustainable fattening of Hu sheep in this region. Result: Results indicated that animals fed the 15.11% CP diet showed a significantly higher average daily gain (ADG) and cumulative weight gain compared with those fed 11.07% or 13.07% CP (p < 0.05). Exploratory multi-omics enrichment analysis demonstrated significant overrepresentation (p < 0.05) of differentially expressed genes and metabolites in key biological pathways—including bile secretion, AMP-activated protein kinase (AMPK) signaling, steroid biosynthesis, peroxisome proliferator-activated receptor (PPAR) signaling, and oxidative stress-related and oxidative phosphorylation. Correlation analyses characterized two hub genes—ATP6AP1 and LOC101119853—that were significantly and negatively correlated with ADG (p < 0.05), whereas two metabolites—calcidiol and ADP—displayed significant positive relationships with ADG (p < 0.05). Pathway-level comparisons further demonstrated that both the 13.07% vs. 15.11% CP and the 11.07% vs. 15.11% CP contrasts yielded significant enrichment in AMPK signaling and steroid biosynthesis. Notably, calcidiol and ADP both declined numerically in the 13.07% vs. 15.11% CP comparison, whereas only ADP reached statistical significance in the 11.07% vs. 15.11% CP contrast. Conclusions: Collectively, under an ME level of 9.4 MJ/kg, a dietary CP concentration of 15.11% contributes to favorable growth of 4-month-old fattening Hu sheep housed in pens in southern Xinjiang. This level is associated with improved growth performance and coordinated regulation of central hepatic regulatory networks—particularly those involved in energy homeostasis and steroidogenesis—thereby supporting metabolic stability without compromising animal health or production efficiency. These findings provide a preliminary molecular basis for precision protein nutrition in Hu sheep feeding systems and offer translational insights for optimizing ruminant nutrition under arid and semi-arid environmental constraints. All correlations indicate potential associations, not causal relationships. Full article
(This article belongs to the Special Issue Metabolic Responses to Feed and Nutrition in Livestock)
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20 pages, 3857 KB  
Article
Dietary Supplementation with Methionine and Lysine Enhances Antioxidant Function and Muscle Quality of Hefang Crucian Carp (Carassius auratus)
by Xiao Chen, Yiren Wang, Xubing Wang, Minggui Jiang, Hui Li, Xingyu Huang, Hanyuan Wang, Qianhong Gu, Yonghua Zhou and Yamei Xiao
Animals 2026, 16(11), 1636; https://doi.org/10.3390/ani16111636 - 27 May 2026
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Abstract
Methionine (Met) and lysine (Lys), as primary limiting amino acids, play important roles in regulating muscle quality in aquatic animals. This study investigated the effects of dietary Met and Lys supplementation on the growth performance, antioxidant function, and muscle quality of Hefang crucian [...] Read more.
Methionine (Met) and lysine (Lys), as primary limiting amino acids, play important roles in regulating muscle quality in aquatic animals. This study investigated the effects of dietary Met and Lys supplementation on the growth performance, antioxidant function, and muscle quality of Hefang crucian carp (HCC) using physiological and transcriptomic analyses. Fish were fed three diets for 8 weeks: a basal diet (LA) and two diets supplemented with DL-methionine at 1.7% (MA) and 3.4% (HA), respectively, while L-lysine supplementation was fixed at 3.4%. The results indicated that dietary Met and Lys supplementation had no significant effect on the growth performance of HCC (p > 0.05), but significantly reduced serum triglyceride (TG) and cholesterol levels (T-CHO) (p < 0.05). Additionally, serum total protein (TP) content was significantly increased in the MA group (p < 0.05). Analysis of serum antioxidant enzyme activities indicated that appropriate Met and Lys supplementation improved antioxidant capacity and upregulated the expression of antioxidant-related genes (Nrf2, GPX1a, GSTO1, GSTP1) in the muscle. Moreover, the MA group exhibited superior muscle hardness and gumminess, while the HA group had higher springiness and chewiness (p < 0.05). Muscle fiber density was significantly increased, whereas diameter and area showed opposite trends in fish fed 1.7% Met and 3.4% Lys (p < 0.05). Furthermore, appropriate Met and Lys supplementation significantly affected muscle fiber development genes (MyoD, MyoG, and MRF4), with MyoG highest in the HA group and MyoD and MRF4 highest in the MA group (p < 0.05). Comparative transcriptomic analysis of muscle tissue showed DEGs were mainly enriched in pathways correlated with muscle quality, involving cardiac muscle contraction, actin cytoskeleton regulation, PPAR signaling pathway and ECM–receptor interaction. Taken together, our findings enhance the understanding of the molecular mechanisms underlying the effects of dietary Met and Lys on muscle quality in HCC, providing valuable insights for the development of nutritional strategies in the aquaculture industry. Full article
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20 pages, 3268 KB  
Article
Transcriptomic Mechanisms Underlying Dietary Fish Oil, Phospholipid, and Vitamin E Supplementation in Promoting Ovarian Development in Leptobotia elongata
by Yuxin Jiang, Yihui Mei, Lin Luo, Wenqi Chang, Jian Gao, Min Guan and Xiaojuan Cao
Animals 2026, 16(11), 1604; https://doi.org/10.3390/ani16111604 - 25 May 2026
Viewed by 707
Abstract
Leptobotia elongata, a rare freshwater fish endemic to China, frequently exhibits retarded ovarian development under artificial captivity, severely constraining large-scale reproduction. This study evaluated the effects of combined dietary supplementation with fish oil (FO), soybean phospholipids (PLs), and vitamin E (VE) on [...] Read more.
Leptobotia elongata, a rare freshwater fish endemic to China, frequently exhibits retarded ovarian development under artificial captivity, severely constraining large-scale reproduction. This study evaluated the effects of combined dietary supplementation with fish oil (FO), soybean phospholipids (PLs), and vitamin E (VE) on ovarian development through a 6-month feeding trial. Hematoxylin and eosin staining revealed that oocytes in the mixed lipid group (MIX: FO + PL + VE) advanced to developmental stage III, whereas oocytes in the control group (CON) were predominantly arrested at stages I–II. Transcriptomic analysis identified 1393 differentially expressed genes (651 upregulated, 742 downregulated). Upregulated genes were enriched in nucleolus- and nuclear pore-related cellular components and RNA-binding molecular functions, indicating enhanced ribosome biogenesis capacity. Downregulated genes were concentrated in DNA damage repair pathways and Mediator complex-mediated transcriptional regulation, suggesting alleviation of oxidative stress. Protein–protein interaction network analysis identified mphosph10, utp11, nat10, emg1, and ftsj3 as core hub genes. Additionally, 44 differentially expressed transcription factors were identified, with Forkhead (forkhead.38), GATA (gata.4), and MYB (myb.40) significantly upregulated, indicating activation of a pro-developmental transcriptional program. These findings provide a theoretical basis for precision lipid nutrition formulation in L. elongata fish diets. Full article
(This article belongs to the Section Aquatic Animals)
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