Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology

Dietary supplementation with farnesol confers a protective effect on the intestine of broiler chickens challenged with lipopolysaccharide by reshaping intestinal flora structure and regulating TLR4/NF-κB signaling pathway

Farnesol (FAN), one of plant essential oils, is widely found in a variety of natural plants. Studies demonstrated that FAN contributed to the antioxidant and immune function as well as improving the intestinal flora, however effects of it on the broiler chickens has not been fully characterized. In the present study, we present an undated report of its effects on growth performance, antioxidant and immune functions of broiler chickens challenged with lipopolysaccharide (LPS). One hundred healthy male AA+ broiler chickens with uniform body weight were divided into control and FAN groups, there were five replicates and 10 birds in each one. The trial lasted for 28 days, and two birds with uniform body weight were selected from each replicate to be treated with intraperitoneal injection of LPS at the end of the trial, and then samples were harvested after 3 h. Results showed that dietary supplementary with FAN tended to improve the feed conversion ratio (FCR) (P = 0.058). The levels of serum lactate dehydrogenase and IL-1β were elevated in the birds challenged with LPS, as well as the content of malondialdehyde in the ileal and liver (P < 0.05). Additionally, LPS treatment descended the levels of catalase and superoxide dismutase, and the ratio of villi height to crypt depth in the ileum (P < 0.05). Dietary supplementation with FAN was able to alleviate the abnormal changes of the above indexes caused by LPS. In addition, dietary supplementation with FAN also contributed to alleviating the up-regulation of Toll-like receptor 4 (TLR-4), nuclear transcription factor κB (NF-κB), myeloid differentiation primary response gene 88 (MYD88), tumor necrosis factor (TNF-α) and IL-1β transcription levels in the ileum and liver of birds challenged with LPS (P < 0.05). Results of intestinal flora demonstrated that the relative abundance of Candidatus Arthromitus was up-regulated in the ileal chyme of birds challenged with LPS, and dietary supplementation with FAN could reshape it. Intriguingly, the relative abundance of Candidatus Arthromitus was positively correlated with the mRNA levels of TLR-4, NF-κB, MYD88, TNF-α and IL-1β in the ileum (P < 0.05). In conclusion, dietary supplementation with FAN might confer a protective effect on the intestine of broiler chickens challenged with lipopolysaccharide by reshaping intestinal flora, especially Candidatus Arthromitus, and regulating TLR4/NF-κB signaling pathway.

Dietary supplementary with ellagic acid improves the intestinal barrier function and flora structure of broiler chicken challenged with E. coli K88

Ellagic acid (EA) contributes to the immunity and anti-oxidant function of body, whereas there are few reports about its effect on the intestinal health and growth performance of broiler chickens. Hence, the present study was arranged to investigate the effect of dietary supplementary with EA on the intestinal barrier function and flora structure of broiler chickens challenged with Escherichia coli K88 (E. coli K88). A total of 216 healthy 1-day-old, Ross 308 broilers with uniform weight were randomly assigned into three treatment groups, six replicates in each group and twelve birds in each replicate. Broilers in the control (CTR) group and E. coli K88 infected group (ETEC) were fed with the basic diet, and 200 mg/kg EA was supplemented into the diet of the E. coli K88 infected group treated with EA (EAETEC). The animal trial had lasted for 42 days, and the outcomes showed that the ADG and ADFI during the animal trial, the jejunal villi height (VH) and the ratio of VH to crypt depth (CD) tended to be decreased with E. coli K88 treated (P< 0.05). Additionally, the level of serum diamine oxidase (DAO) and intestinal malondialdehyde (MDA) were elevated, the activity of intestinal total superoxide dismutase (T-SOD) and glutathione peroxidase (GSH-Px), the mRNA levels in jejunal claudin-1 and occludin were down-regulated with E. coli K88 treated as well as the transcription levels of ileal Mucin-2, aquaporin-3 (AQP-3) and Na+/H+ exchanger proteins-3 (NHE-3) (P< 0.05). In addition, E. coli K88 down-regulated the α-diversity index of cecal flora, the ratio of Bacteroidota to Firmicutes and the relative abundance of Barnesiella were up-regulated and it of Alistipes was descended with E. coli K88 treated (P< 0.05). Beyond that, the content of propionic acid in the cecal chyme was decreased and the amino acid metabolic pathways were inhibited with E. coli K88 challenged (P< 0.05). Additionally, there was a significant positive correlation between the relative abundance of Alistipes and the levels of butyric acid in the caecal chyme and the activity of GSH-Px in the intestine (P< 0.05). Interestingly, dietary supplementary with EA could reshape the intestinal flora structure and alleviate the above negative effects of E. coli K88 on broiler chickens. In conclusion, dietary supplementary with ellagic acid improved the intestinal barrier function and flora structure of broiler chickens challenged with E. coli K88.

Dietary supplementation with N-acetylcysteine confers a protective effect on muscle and liver in lipopolysaccharide-challenged piglets

N-acetylcysteine (NAC) is a well-established antioxidant that offers exciting opportunities for intestinal health in weaned piglets, while the effects of NAC on muscle and liver has not been fully characterized. Therefore, the present study was performed to investigate the effects of dietary supplementation with NAC on muscle and liver in weaned piglets challenged with lipopolysaccharide (LPS). Twenty-four piglets (24-day-old) were randomly assigned to three treatment groups, the piglets in the control (CTR) and LPS- challenged (LPS) groups were fed the basal diet and those in the LPS+ NAC group was fed the basal diet supplemented with 500 mg/kg NAC. The animal trial lasted for 21 days. At the end of the trial, piglets in the LPS and LPS+ NAC groups were injected intraperitoneally with LPS (100 μg/kg body weight) and piglets in the CTR group were administrated with an equal volume of normal saline. 3 h later, the blood was collected and tissue samples were obtained after 6 h of LPS or normal saline treatment. The results showed that the level of IL-1β, and the mRNA levels of C-X-C motif chemokine receptor 3 (CXCR3) and interferon-γ (IFN-γ) in the liver were up-regulated, and the mRNA levels of insulin-like growth factor 1 (IGF-1), total glutathione (T-GSH), and the ratio of total protein to DNA in the liver were decreased under LPS challenge (P < 0.05). At the same time, LPS increased the level of H2O2 and decreased the content of T-GSH and DNA in the longissimus dorsi and gastrocnemius muscles (P < 0.05). In addition, the percentage of monocytes and the level of epidermal growth factor (EGF) were down-regulated in the LPS treatment (P < 0.05). Interestingly, dietary NAC supplementation reversed the above changes induced by LPS (P < 0.05). Furthermore, NAC might alleviate the muscle and liver injury in LPS-challenged piglets by regulating the expression of genes related to the type I interferon signaling pathway, as well as hypoxia inducible factor 1 (HIF1) and nuclear factor erythroid-2 related factor 2 (Nrf-2). Our findings suggested that dietary supplementation with NAC could benefit the health of muscle and liver in LPS-challenged weaned piglets.

Post-stroke cognitive impairment: exploring molecular mechanisms and omics biomarkers for early identification and intervention

Post-stroke cognitive impairment (PSCI) is a major stroke consequence that has a severe impact on patients' quality of life and survival rate. For this reason, it is especially crucial to identify and intervene early in high-risk groups during the acute phase of stroke. Currently, there are no reliable and efficient techniques for the early diagnosis, appropriate evaluation, or prognostication of PSCI. Instead, plenty of biomarkers in stroke patients have progressively been linked to cognitive impairment in recent years. High-throughput omics techniques that generate large amounts of data and process it to a high quality have been used to screen and identify biomarkers of PSCI in order to investigate the molecular mechanisms of the disease. These techniques include metabolomics, which explores dynamic changes in the organism, gut microbiomics, which studies host-microbe interactions, genomics, which elucidates deeper disease mechanisms, transcriptomics and proteomics, which describe gene expression and regulation. We looked through electronic databases like PubMed, the Cochrane Library, Embase, Web of Science, and common databases for each omics to find biomarkers that might be connected to the pathophysiology of PSCI. As all, we found 34 studies: 14 in the field of metabolomics, 5 in the field of gut microbiomics, 5 in the field of genomics, 4 in the field of transcriptomics, and 7 in the field of proteomics. We discovered that neuroinflammation, oxidative stress, and atherosclerosis may be the primary causes of PSCI development, and that metabolomics may play a role in the molecular mechanisms of PSCI. In this study, we summarized the existing issues across omics technologies and discuss the latest discoveries of PSCI biomarkers in the context of omics, with the goal of investigating the molecular causes of post-stroke cognitive impairment. We also discuss the potential therapeutic utility of omics platforms for PSCI mechanisms, diagnosis, and intervention in order to promote the area's advancement towards precision PSCI treatment.

Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management

Molecular docking is a computational technique that predicts the binding affinity of ligands to receptor proteins. Although it has potential uses in nutraceutical research, it has developed into a formidable tool for drug development. Bioactive substances called nutraceuticals are present in food sources and can be used in the management of diseases. Finding their molecular targets can help in the creation of disease-specific new therapies. The purpose of this review was to explore molecular docking's application to the study of dietary supplements and disease management. First, an overview of the fundamentals of molecular docking and the various software tools available for docking was presented. The limitations and difficulties of using molecular docking in nutraceutical research are also covered, including the reliability of scoring functions and the requirement for experimental validation. Additionally, there was a focus on the identification of molecular targets for nutraceuticals in numerous disease models, including those for sickle cell disease, cancer, cardiovascular, gut, reproductive, and neurodegenerative disorders. We further highlighted biochemistry pathways and models from recent studies that have revealed molecular mechanisms to pinpoint new nutraceuticals' effects on disease pathogenesis. It is convincingly true that molecular docking is a useful tool for identifying the molecular targets of nutraceuticals in the management of diseases. It may offer information about how nutraceuticals work and support the creation of new therapeutics. Therefore, molecular docking has a bright future in nutraceutical research and has a lot of potentials to lead to the creation of brand-new medicines for the treatment of disease.

Effects of tannic acid on the immunity and intestinal health of broiler chickens with necrotic enteritis infection

BACKGROUND

In broiler chickens, necrotic enteritis (NE) infection can reduce production performance. Tannic acid has shown great potential as a treatment of NE in broilers. However, the appropriate dosage of tannic acid in NE of broilers and the improvement effect on intestinal health are not very clear. In this study, we aimed to investigate the effects of different doses of tannic acid on the production performance, immunity, and intestinal health of broilers by constructing an NE model with C. perfringens infection and determining the appropriate dosage of tannic acid with regard to NE.

RESULTS

Challenged birds showed significant reduction in body weight, villus height, and the ratio of villus height to crypt depth (P < 0.05) and increase in the feed consumption gain ratio, intestinal lesion score, and crypt depth (P < 0.05). The infection significantly reduced the relative Bacteroidota and Ligilactobacillus abundance (P < 0.05) and increased the ratio of Firmicutes/Bacteroidota and cecal content of C. perfringens (P < 0.05). Challenged birds fed diets supplemented with tannic acid showed significantly increased mRNA expression of nutrient transport carriers and intestinal barrier genes and growth performance and reduced serum zonulin and endotoxin levels (P < 0.05). Addition of tannic acid to the diet inhibited the inflammatory response by reducing the number of coccidia oocysts in feces and the content of C. perfringens in the cecum. Specifically, tannic acid reduced the serum levels of C reactive protein, myeloperoxidase, and specific IgY and ileal mucosal secretory immunoglobulin A levels in the ileal mucosa compared with those in the NE-infected birds. NE-infected birds fed diets supplemented with tannic acid also showed significantly increased relative Anaerocolumna, Thermoanaerobacterium, and Thermosinus abundance (P < 0.05); their microbial composition and functional predictions were similar to those of the NC group.

CONCLUSIONS

Tannic acid in the diet alleviated NE by enhancing the intestinal barrier and absorption function. The recommended dietary tannic acid additive level is 500-750 mg/kg. Our study findings would be useful in reducing related economic losses in the broiler industry.

Dietary Lactobacillus fermentum and Lactobacillus paracasei improve the intestinal health of broilers challenged with coccidia and Clostridium perfringens

Necrotic enteritis (NE) is a great threat to the intestinal health of broilers, resulting in decreased growth performance and significant economic losses. Lactobacillus fermentum (LF) and Lactobacillus paracasei (LP) exert beneficial effects on intestinal health. The aim of the present study was to investigate the effects of dietary LF and LP on the intestinal health and growth performance of broilers challenged with coccidia and Clostridium perfringens (CCP). The animal trial was carried out using 336 broilers (Ross 308) for 35 days with a completely randomized design. The broilers were divided into 4 groups based on treatment as follows: the control (CTR) group was fed the basal diet and without CCP challenge and the CCP group was fed the basal diet and with CCP challenge. The broilers in the CCP+LF and CCP+LP groups were challenged by CCP, and meanwhile, LF (1 × 10⁹ CFU/g) and LP (1 × 10⁹ CFU/g) were supplemented into the basal diets, respectively. The results showed that the growth performance and the intestinal morphology were negatively affected by the CCP challenge. In addition, the number of coccidia in the intestinal digesta and the relative abundance of Escherichia coli in the cecal digesta were increased. Besides, the mRNA level of IgA in the jejunum was downregulated, and the transcript level of IL-8 was upregulated by the CCP challenge. Dietary LF and LP failed to improve the growth performance of broilers with the CCP challenge. However, they were beneficial for intestinal barrier function. In addition, dietary LF was able to alleviate the downregulation of TGF-β mRNA level in the spleen with CCP challenge and decreased the lesion scores compared with the CCP group. Furthermore, dietary LP alleviated the upregulation of the IL-8 mRNA level in the jejunum with CCP challenge and reduced the number of coccidia in the ileal digesta. In conclusion, dietary LF and LP failed to mitigate the negative effects of CCP infection on growth performance; however, they were able to improve the intestinal health of broilers challenged with CCP by strengthening the intestinal barrier and alleviating inflammation.

The Effect of the Restrictive Ketogenic Diet on the Body Composition, Haematological and Biochemical Parameters, Oxidative Stress and Advanced Glycation End-Products in Young Wistar Rats with Diet-Induced Obesity

Over the past few years, the interest in the application of the ketogenic diet (KD) for obesity management is growing. Although many studies have been performed on the effects of KD, the metabolic and physiological impact of KD is still not fully understood. Therefore, this study aimed to evaluate the effect of calorie-restricted KD on the body weight and composition, oxidative stress, and advanced glycation end products (AGEs) assessed in an animal model with young Wistar rats. KD was followed for 4 weeks in maturity after an obesity-inducing high-fat diet during adolescence, resulting in a slowing down of the weight gain but higher adiposity compared to a standard diet. Increased adiposity resulted in an deterioration of liver parameters, suggesting negative changes in this organ. No adverse effects of KD were determined in haematological parameters in young rats. KD did not affect AGEs; however, a decrease in oxidative stress was observed. Based on the presented results, it can be concluded that KD applied for weight loss in obesity induced in adolescence may reduce oxidative stress without compromising the haematological status; however, caution may be required to control adiposity, glucose level and liver health. Thus, KD therapy should be carefully controlled, especially in young subjects.

Construction of low intestinal bacteria model and its effect on laying performance and immune function of laying hens

The objective of this study was to establish a low-bacteria intestinal model in chickens, and then to investigate the characteristics involving in immune function and intestinal environment of this model. A total of 180 twenty-one-week-old Hy-line gray layers were randomly allocated into 2 treatment groups. Hens were fed with a basic diet (Control), or an antibiotic combination diet (ABS) for 5 weeks. Results showed that the total bacteria in the ileal chyme were significantly dropped after ABS treatment. Compared with the Control group, the genus-level bacteria such as Romboutsia, Enterococcus, and Aeriscardovia were reduced in the ileal chyme of the ABS group (P < 0.05). In addition, the relative abundance of Lactobacillus_delbrueckii, Lactobacillus_aviarius, Lactobacillus_gasseri, and Lactobacillus_agilis in the ileal chyme were also descended (P < 0.05). However, Lactobacillus_coleohominis, Lactobacillus_salivarius, and Lolium_perenne were elevated in the ABS group (P < 0.05). Beyond that, ABS treatment decreased the levels of interleukin-10 (IL-10) and β-defensin 1 in the serum, as well as the number of goblet cells in the ileal villi (P < 0.05). Additionally, the genes mRNA levels of the ileum such as Mucin2, Toll-like receptors 4 (TLR4), Myeloid differentiation factor 88 (MYD88), NF-κB, IL-1β, Interferon-gama (IFN-γ), IL-4 and the ratio of IFN-γ to IL-4 were also down-regulated in the ABS group (P < 0.05). In addition, there were no significant changes about egg production rate and egg quality in the ABS group. In conclusion, dietary supplemental antibiotic combination for 5 weeks could establish a low intestinal bacteria model of hens. The establishment of a low intestinal bacteria model did not affect the egg-laying performance, while caused immune suppression in laying hens.

Effects of dietary L-Proline and L-Alanine on growth performance, and flesh quality of common carp (Cyprinus carpio) juveniles

The purpose of the present study was to investigate the effects of amino acids L-Proline and LAlanine on growth performance, amino acid, and fatty acid levels in the fillet of juvenile common carp. 450 juvenile common carp were randomly distributed in 30 tanks and fed with three levels of proline (5 [P5], 10 [P10], and 15 [P15] g/kg), three levels of Alanine [A] (5 [A5], 10 [A10], and 15 [A15] g/kg), three levels of proline-alanine combination [PA] (2.5 + 2.5 [2.5PA], 5 + 5 [5PA], 7.5 + 7.5 [7.5PA] g/kg feed) and basal diet (control). The highest body weight gain (25.85 ± 0.1 g) and survival rate (91.11 ± 3.84) were observed in 7.5 PA treatment. The highest protein content (64.58 ± 0.49) was noticed in 2.5 PA; however, compared to combined treatments (5 PA and 2.5 PA), it did not show any significant difference (p<0.05). The highest total amount of essential amino acids (48.30 ± 48.3) were observed in 7.5 PA treatment. The highest amount of DHA (5.65 ± 0.08), total EPA, and DHA (8.91 ± 0.13) were in 7.5 PA treatment. Finally, it can be concluded that two amino acids of L-Proline and L-Alanine at the combined level of 5 PA can improve the growth performance, survival, and fillet composition in the juvenile common carp.

Soya saponin fails to improve the antioxidation and immune function of laying hens with antibiotics treated

Soya saponin (SS) helps to improve antioxidant and immune function of body, and intestinal bacteria might play an important role here. In the present study, the co-occurring network of the ileal flora was analyzed with 50 mg/kg SS supplemented to the diet, and Romboutsia was found to have evolved into a dominant flora. In addition, the co-occurring network of the flora was changed with the combined antibiotic treated, and the unidentified-cyanobacteria developed into the dominant flora, whereas the relative abundance of Romboutsia was dropped. Dietary SS failed to elevate the relative abundance of Romboutsia with antibiotics treated, at the same time, it was not helpful for the antioxidant and immune function of laying hens. While dietary SS had a little help on the egg-laying performance. Intestinal bacteria did play a key role in the biological functions of SS on laying hens. In conclusion, SS failed to improve the antioxidation and immune function of laying hens with antibiotics treated.

Fecal Microbiota Transplantation Reshapes the Physiological Function of the Intestine in Antibiotic-Treated Specific Pathogen-Free Birds

The topic about the interactions between host and intestinal microbiota has already caught the attention of many scholars. However, there is still a lack of systematic reports on the relationship between the intestinal flora and intestinal physiology of birds. Thus, this study was designed to investigate it. Antibiotic-treated specific pathogen-free (SPF) bird were used to construct an intestinal bacteria-free bird (IBF) model, and then, the differences in intestinal absorption, barrier, immune, antioxidant and metabolic functions between IBF and bacteria-bearing birds were studied. To gain further insight, the whole intestinal flora of bacteria-bearing birds was transplanted into the intestines of IBF birds to study the remodeling effect of fecal microbiota transplantation (FMT) on the intestinal physiology of IBF birds. The results showed that compared with bacteria-bearing birds, IBF birds had a lighter body weight and weaker intestinal absorption, antioxidant, barrier, immune and metabolic functions. Interestingly, FMT contributed to reshaping the abovementioned physiological functions of the intestines of IBF birds. In conclusion, the intestinal flora plays an important role in regulating the physiological functions of the intestine.

Omics Technology for the Promotion of Nutraceuticals and Functional Foods

The influence of nutrition and environment on human health has been known for ages. Phytonutrients (7,000 flavonoids and phenolic compounds; 600 carotenoids) and pro-health nutrients—nutraceuticals positively add to human health and may prevent disorders such as cancer, diabetes, obesity, cardiovascular diseases, and dementia. Plant-derived bioactive metabolites have acquired an imperative function in human diet and nutrition. Natural phytochemicals affect genome expression (nutrigenomics and transcriptomics) and signaling pathways and act as epigenetic modulators of the epigenome (nutri epigenomics). Transcriptomics, proteomics, epigenomics, miRNomics, and metabolomics are some of the main platforms of complete omics analyses, finding use in functional food and nutraceuticals. Now the recent advancement in the integrated omics approach, which is an amalgamation of multiple omics platforms, is practiced comprehensively to comprehend food functionality in food science.

Dietary Saccharomyces cerevisiae improves intestinal flora structure and barrier function of Pekin ducks

This study aimed at investigating the effects of dietary Saccharomyces cerevisiae (SC) on the intestinal flora structure and barrier function of Pekin duck. A total of 180 1-day-old Pekin ducks were randomly divided into 3 groups with 6 replicates in each group and 10 birds per replicate. The birds in the control group (CON) were fed the basal diet, and those in the experimental group were fed the basal diets supplemented with 600 mg/kg SC (LSC) and 1,200 mg/kg (HSC), respectively. The trial lasted for 42 d. Results showed that LSC and HSC treatments tended to improve the feed conversion efficiency during the trial. The ileum length of birds in the LSC and HSC groups was elevated. Additionally, with 600mg/kg SC supplemented, the mRNA levels of villin, claudin3, and MUC 2 in d21 were up-regulated, as well as the mRNA levels of villin, claudin3, occludin, i-FABP, ZO-1, and MUC 2 in d42. In addition, dietary SC supplementation improved the α-diversity of the bacteria in cecal chyme and tended to increase the abundance (RA) of Bacteroidetes (P = 0.071). Besides, the RA of Ruminococcaceae_UCG-014 was raised in the LSC group. Beyond that, the RA of Proteobacteria was descended with two levels of SC added. In conclusion, dietary Saccharomyces cerevisiae, particularly at 600 mg/kg level, improved the intestinal flora structure and barrier function of Pekin duck.

Dietary soya saponin improves the lipid metabolism and intestinal health of laying hens

Soya saponin (SS) is a natural active substance of leguminous plant, which could improve lipid metabolism and regulate immune function. Intestinal flora might play a key role in the biological functions of SS. The objective of this study was to measure the effects of dietary SS on immune function, lipid metabolism, and intestinal flora of laying hens with or without antibiotic treated. The experiment was designed as a factorial arrangement of 3 dietary SS treatments × 2 antibiotic treatments. Birds were fed a basal diet (CON) or a low-SS diet (50 SS) containing 50 mg/kg SS, or a high-SS diet (500 SS) containing 500 mg/kg SS. Birds were cofed with or without antibiotics. The growth experiment lasted for 10 wk. Results showed that birds fed the 50 mg/kg SS diet tended to have lower abdominal fat rate. The gene expression of liver X receptor-α (LxR-α) in liver and serum total cholesterol (TC) were dropped, and the gene expression of acyl-CoA thioesterase 8 (ACOT8) in liver were upregulated. Compared with CON group, the levels of lysozyme, IL-10, and transforming growth factor (TGF-β) in the serum were elevated as along with gene expression of IL-10, TGF-β, and LYZ in ileum of both 50 and 500 SS group. However, the level of secretory immunoglobulin A (sIgA) and Mucin-2 in the ileum were downregulated in the 500 SS group. Additionally, Lactobacillus and Lactobacillus gasseri were the dominant bacteria in the 50 SS group, whereas the relative abundance of Lactobacillus was dropped in the 500 SS group. With combined antibiotics treatment, the α-diversity of bacteria was reduced, and the biological effects of SS were eliminated. In conclusion, the lipid metabolism, immune function, and intestinal flora of the laying hens were improved with the dietary supplementation of 50 mg/kg SS. But dietary 500 mg/kg SS had negative effects on laying hens.

Soya saponin improves egg-laying performance and immune function of laying hens

BACKGROUND

Soya saponin (SS), an active compound in soybean meals, has been widely studied in the medical field. However, it was considered as an anti-nutritional factor in poultry diets. The objective of this experiment was to measure the effects of dietary SS using three dietary treatments on egg-laying performance and immune function of laying hens. Birds were fed a low soybean meal basal diet (CON), a low-SS diet (50 SS) containing 50 mg/kg SS, or a high-SS diet (500 SS) containing 500 mg/kg SS for 10 weeks. At the end of the 5th and 10th week of the trial, samples were collected for analysis.

RESULTS

Results showed that with 50 mg/kg SS supplementation, the egg production rate, feed conversion ratio (FCR), and eggshell quality tended to be improved. Serum follicle stimulating hormone (FSH) and Interleukin-4 (IL-4) levels were also elevated as well as the peripheral blood LPS stimulation index, the proportion of B lymphocytes, and antibody titer of bovine serum albumin (BSA). We also found that mRNA levels of follicle stimulating hormone receptor (FSHR) in ovarian, nuclear transcription factor kappa B (NF-κB), Transforming growth factor (TGF-β) and interferon γ (IFN-γ) in spleen were up-regulated at the end of the trial. Additionally, dietary 50 mg/kg SS improved the ileal flora via up-regulating the relative abundance of Lactobacillus, Romboutsia and Lactobacillus delbrueckii. Although the immune related indicators were improved with 500 mg/kg SS supplemented, it seemed to have a negative influence on the laying-performance. Specifically, serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), and the ratio of IFN-γ to IL-4 were increased in the 500 SS group at the end of the trial. The mRNA levels of gonadotropin releasing hormone 1 (GnRH1) in Hypothalamus, the estrogen related receptor (ERR) in ovaries were downregulated as well as the egg production rate during the trial with 500 mg/kg SS supplemented.

CONCLUSIONS

The egg production performance was improved by dietary supplemented with 50 mg/kg SS via increasing ovarian FSHR transcription level and serum estrogen level. A beneficial shift in intestinal microflora was recorded, and the immune function of laying hens was also improved with 50 mg/kg SS supplementation. Surprisingly, the long-term supplementation of 500 mg/kg SS exerted a negative impact on the laying performance and physiological functions of the liver of laying hens.

Data analysis methods for defining biomarkers from omics data

Omics mainly includes genomics, epigenomics, transcriptomics, proteomics and metabolomics. The rapid development of omics technology has opened up new ways to study disease diagnosis and prognosis and to define prospective information of complex diseases. Since omics data are usually large and complex, the method used to analyze the data and to define important information is crucial in omics study. In this review, we focus on advances in biomarker discovery methods based on omics data in the last decade, and categorize them as individual feature analysis, combinatorial feature analysis and network analysis. We also discuss the challenges and perspectives in this field.

Dietary supplementation with L-arginine between days 14 and 25 of gestation enhances NO and polyamine syntheses and the expression of angiogenic proteins in porcine placentae

Dietary supplementation with 0.4 or 0.8% L-arginine (Arg) to gilts between days 14 and 25 of gestation enhances embryonic survival and vascular development in placentae; however, the underlying mechanisms are largely unknown. This study tested the hypothesis that Arg supplementation stimulated placental expression of mRNAs and proteins that enhance angiogenesis, including endothelial nitric oxide synthase (eNOS), vascular endothelial growth factor (VEGF), placental growth factor (PGF), GTP cyclohydrolase-I (GTP-CH1), ornithine decarboxylase (ODC1), and vascular endothelial growth factor receptors 1 and 2 (VEGFR1 and VEGFR2). Beginning on the day of breeding, gilts were fed daily 2 kg of a corn-soybean meal-based diet supplemented with 0.0 (control), 0.4, or 0.8% Arg. On day 25 of gestation, gilts were hysterectomized to obtain uteri and conceptuses for histochemical and biochemical analyses. eNOS and VEGFR1 proteins were localized to endothelial cells of maternal uterine blood vessels and to the uterine luminal epithelium, respectively. Compared with the control, dietary supplementation with 0.4 or 0.8% Arg increased (P < 0.05) the amounts of nitrite plus nitrate (NOx; oxidation products of NO) and polyamines in allantoic and amniotic fluids, concentrations of NOx, tetrahydrobiopterin (BH4, an essential cofactor for all NOS isoforms) and polyamines in placentae, as well as placental protein abundances of GTP-CH1 (the key enzyme for BH4 production) and ODC1 (the key enzyme for polyamine synthesis). Placental  mRNA levels for GTP-CH1, eNOS, PGF, VEGF, and VEGFR2 increased in response to both 0.4% and 0.8% Arg supplementation. Collectively, these results indicate that dietary Arg supplementation to gilts between days 14 and 25 of pregnancy promotes placental angiogenesis by increasing the expression of mRNAs and proteins for angiogenic factors as well as NO and polyamine syntheses.

Statistical and Machine-Learning Analyses in Nutritional Genomics Studies

Nutritional compounds may have an influence on different OMICs levels, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and metagenomics. The integration of OMICs data is challenging but may provide new knowledge to explain the mechanisms involved in the metabolism of nutrients and diseases. Traditional statistical analyses play an important role in description and data association; however, these statistical procedures are not sufficiently enough powered to interpret the large integrated multiple OMICs (multi-OMICS) datasets. Machine learning (ML) approaches can play a major role in the interpretation of multi-OMICS in nutrition research. Specifically, ML can be used for data mining, sample clustering, and classification to produce predictive models and algorithms for integration of multi-OMICs in response to dietary intake. The objective of this review was to investigate the strategies used for the analysis of multi-OMICs data in nutrition studies. Sixteen recent studies aimed to understand the association between dietary intake and multi-OMICs data are summarized. Multivariate analysis in multi-OMICs nutrition studies is used more commonly for analyses. Overall, as nutrition research incorporated multi-OMICs data, the use of novel approaches of analysis such as ML needs to complement the traditional statistical analyses to fully explain the impact of nutrition on health and disease.

Impacts and Echoes: The Lasting Influence of the White House Conference on Food, Nutrition, and Health

The 1969 White House Conference on Food, Nutrition, and Health had a significant influence on the direction of food and nutrition policy in the United States. The conference produced recommendations leading to federal legislation and programs to alleviate hunger and malnutrition, improve consumers' nutrition knowledge through education and labeling, and monitor the nutritional status of the population. Fifty years later, its legacy was revisited at a conference convened by Harvard University and Tufts University. This article reviews the literature contributing to the first author's keynote speech at the conference, its influencers, and its influences. We focus on the highlights of five domains that set the stage for the conference: the social environment, the food environment, nutrition science, public health data, and policy events. We briefly describe the conference, its proposed directions, and its lasting legacy in these five domains.

Composition of amino acids and related nitrogenous nutrients in feedstuffs for animal diets

We analyzed the composition of amino acids (AAs) in oligopeptides, proteins, and the free pool, as well as creatine, agmatine, polyamines, carnosine, anserine, and glutathione, in animal- and plant-derived feedstuffs. Ingredients of animal origins were black soldier fly larvae meal (BSFM), chicken by-product meal, chicken visceral digest, feather meal, Menhaden fishmeal, Peruvian anchovy fishmeal, Southeast Asian fishmeal, spray-dried peptone from enzymes-treated porcine mucosal tissues, poultry by-product meal (pet-food grade), spray-dried poultry plasma, and spray-dried egg product. Ingredients of plant origins were algae spirulina meal, soybean meal, and soy protein concentrate. All animal-derived feedstuffs contained large amounts of all proteinogenic AAs (particularly glycine, proline, glutamate, leucine, lysine, and arginine) and key nonproteinogenic AAs (taurine and 4-hydroxyproline), as well as significant amounts of agmatine, polyamines, creatine, creatinine, creatine phosphate, and glutathione. These nitrogenous substances are essential to either DNA and protein syntheses in cells or energy metabolism in tissues (particularly the brain and skeletal muscle). Of note, chicken by-product meal, poultry by-product meal, and spray-dried poultry plasma contained large amounts of carnosine and anserine (potent antioxidants). Compared with most of the animal-derived feedstuffs, plant-derived feedstuffs contained much lower contents of glycine and proline, little 4-hydroxyproline, and no creatine, creatinine, creatine phosphate, carnosine or anserine. These results indicate the unique importance of animal-source feedstuffs in improving the feed efficiency, growth and health of animals (including fish and companion animals). Because soy protein concentrate is consumed by infants, children and adults, as are BSFM and algae for children and adults, our findings also have important implications for human nutrition.

Microarray analysis reveals the inhibition of intestinal expression of nutrient transporters in piglets infected with porcine epidemic diarrhea virus

Porcine epidemic diarrhea virus (PEDV) infection can induce intestinal dysfunction, resulting in severe diarrhea and even death, but the mode of action underlying these viral effects remains unclear. This study determined the effects of PEDV infection on intestinal absorption and the expression of genes for nutrient transporters via biochemical tests and microarray analysis. Sixteen 7-day-old healthy piglets fed a milk replacer were randomly allocated to one of two groups. After 5-day adaption, piglets (n = 8/group) were orally administrated with either sterile saline or PEDV (the strain from Yunnan province) at 10^4.5 TCID₅₀ (50% tissue culture infectious dose) per pig. All pigs were orally infused D-xylose (0.1 g/kg BW) on day 5 post PEDV or saline administration. One hour later, jugular vein blood samples as well as intestinal samples were collected for further analysis. In comparison with the control group, PEDV infection increased diarrhea incidence, blood diamine oxidase activity, and iFABP level, while reducing growth and plasma D-xylose concentration in piglets. Moreover, PEDV infection altered plasma and jejunal amino acid profiles, and decreased the expression of aquaporins and amino acid transporters (L-type amino acid transporter 1, sodium-independent amino acid transporter, B(°^,+)-type amino acid transport protein, sodium-dependent neutral amino acid transporter 1, sodium-dependent glutamate/aspartate transporter 3, and peptide transporter (1), lipid transport and metabolism-related genes (lipoprotein lipase, apolipoprotein A1, apolipoprotein A4, apolipoprotein C2, solute carrier family 27 member 2, solute carrier family 27 member 4, fatty acid synthase, and long-chain acyl-CoA synthetase (3), and glucose transport genes (glucose transporter-2 and insulin receptor) in the jejunum. However, PEDV administration increased mRNA levels for phosphoenolpyruvate carboxykinase 1, argininosuccinate synthase 1, sodium/glucose co-transporter-1, and cystic fibrosis transmembrane conductance regulator in the jejunum. Collectively, these comprehensive results indicate that PEDV infection induces intestinal injury and inhibits the expression of genes encoding for nutrient transporters.

Protection against diabetic cardiomyopathy is achieved using a combination of sulforaphane and zinc in type 1 diabetic OVE26 mice

Sulforaphane (SFN) can effectively induce nuclear factor E2-related factor 2 (Nrf2), and zinc (Zn) can effectively induce metallothionein (MT), both of which have been shown to protect against diabetic cardiomyopathy (DCM). However, it is unclear whether combined treatment with SFN and Zn offers better cardiac protection than either one alone. Here, we treated 5-week-old OVE mice that spontaneously develop type 1 diabetes with SFN and/or Zn for 18 weeks. Cardiac dysfunction, by echocardiography, and pathological alterations and remodelling, shown by cardiac hypertrophy, fibrosis, inflammation and oxidative damage, examined by histopathology, Western blotting and real-time PCR, were observed in OVE mice. All these dysfunction and pathological abnormalities seen in OVE mice were attenuated in OVE mice with treatment of either SFN, Zn or SFN/Zn, and the combined treatment with SFN/Zn was better than single treatments at ameliorating DCM. In addition, combined SFN and Zn treatment increased Nrf2 function and MT expression in the heart of OVE mice to a greater extent than SFN or Zn alone. This indicates that the dual activation of Nrf2 and MT by combined treatment with SFN and Zn may be more effective than monotherapy at preventing the development of DCM via complementary, additive mechanisms.

Rapid removal of dextran sulfate sodium from tissue RNA preparations for measurement of inflammation biomarkers

Dextran sulfate sodium (DSS) present in the tissues of DSS-treated laboratory animals inhibits quantitative real-time qPCR (RT-qPCR) and thus may be source of experimental errors. A recent systematic review concluded that the reporting of experimental method was insufficient in a majority of DSS studies and contributed to the poor reproducibility of experiments. Here we compared two DSS cleanup protocols applied to mouse tissue RNA preparations based on silica membrane spin column and lithium chloride precipitation. In absence of cleanup, exogenous DSS significantly inhibited reverse transcription and cDNA amplification at concentrations of 5 × 10^-3 g/L and above during the quantification of IL8 mRNA levels in THP-1 macrophages. Silica membrane spin columns removed DSS from mouse RNA preparations and eliminated DSS-induced inhibition of qPCR. Mouse RNA isolated from DSS-treated tissues and purified with silica membrane spin columns was suitable for RT-qPCR and assessment of inflammatory biomarkers.

Challenges of the heterogeneous nutrition response: interpreting the group mean

Extensive research demonstrates unequivocally that nutrition plays a fundamental role in maintaining health and preventing disease. In parallel nutrition research provides evidence that the risks and benefits of diet and lifestyle choices do not affect people equally, as people are inherently variable in their responses to nutrition and associated interventions to maintain health and prevent disease. To simplify the inherent complexity of human subjects and their nutrition, with the aim of managing expectations for dietary guidance required to ensure healthy populations and individuals, nutrition researchers often seek to group individuals based on commonly used criteria. This strategy relies on demonstrating meaningful conclusions based on comparison of group mean responses of assigned groups. Such studies are often confounded by the heterogeneous nutrition response. Commonly used criteria applied in grouping study populations and individuals to identify mechanisms and determinants of responses to nutrition often contribute to the problem of interpreting the results of group comparisons. Challenges of interpreting the group mean using diverse populations will be discussed with respect to studies in human subjects, in vivo and in vitro model systems. Future advances in nutrition research to tackle inter-individual variation require a coordinated approach from funders, learned societies, nutrition scientists, publishers and reviewers of the scientific literature. This will be essential to develop and implement improved study design, data recording, analysis and reporting to facilitate more insightful interpretation of the group mean with respect to population diversity and the heterogeneous nutrition response.

Composition of polyamines and amino acids in plant-source foods for human consumption

Dietary polyamines and amino acids (AAs) are crucial for human growth, development, reproduction, and health. However, the scientific literature shows large variations in polyamine and AA concentrations among major staple foods of plant origin, and there is a scarcity of information regarding their complete composition of AAs. To provide a much-needed database, we quantified polyamines, agmatine, and AAs in select plant-source foods. On the dry matter basis, total polyamines were most abundant in corn grains, followed by soybeans, sweet potatoes, pistachio nuts, potatoes, peanuts, wheat flour and white rice in descending order. Glutamine was the most abundant AA in pistachio nuts, wheat flour and white rice, arginine in peanuts, leucine in corn grains, glutamate in soybeans, and asparagine in potatoes and sweet potatoes. Glutamine was the second most abundant AA in corn grains, peanuts, potatoes, and soybeans, arginine in pistachio nuts, proline in wheat flour, and glutamate in sweet potatoes and white rice. Free AAs represented ≤ 3.1% of total AAs in corn grains, peanuts, pistachio nuts, soybeans, wheat flour and white rice, but 34.4% and 28.5% in potatoes and sweet potatoes, respectively. Asparagine accounted for 32.3%, 17.5%, and 19.4% of total free AAs in potatoes, sweet potatoes, and white rice, respectively. The content of histidine, glycine, lysine, tryptophan, methionine, cysteine, and threonine was relatively low in corn grains, potatoes, sweet potatoes, and white rice. All of the analyzed plant-source foods lacked taurine, creatine, carnosine and anserine (antioxidants that are abundant in meats and also present in milk), and contained little 4-hydroxyproline. Proper proportions of plant- and animal-source products are likely most desirable for optimizing human nutrition and health.

Optimal Dietary Ferulic Acid for Suppressing the Obesity-Related Disorders in Leptin-Deficient Obese C57BL/6J -ob/ob Mice

Ferulic acid (FA) is a major polyphenolic compound and has been shown to improve the glucose and lipid homeostasis in high-fat diet-induced obese mice. Here, we found the optimal level of dietary FA to ameliorate obesity and obesity-correlated disorders, and identified the responses of gut microbiota to dietary FA in genetic leptin-deficient obese ( ob/ob) mice. The ob/ob mice exhibited persistent higher body weights, feed efficiency, white adipose tissue weights, and hepatic lipid accumulation, compared to those of the wild-type mice. However, 0.5% dietary FA suppressed these symptoms in ob/ob mice. The diversity of gut microbiota and the total abundance of obesity- and anti-obesity-related genera were not influenced after FA intervention in ob/ob mice. These data suggest that sufficient intake of FA (0.5%) could be useful for treating obesity or obesity-related diseases, and this weight-control effect is possibly not correlated with the gut-brain axis.

Dietary l-Tryptophan Supplementation Enhances the Intestinal Mucosal Barrier Function in Weaned Piglets: Implication of Tryptophan-Metabolizing Microbiota

l-Tryptophan (Trp) is known to play an important role in the health of the large intestine. However, a role of dietary Trp in the small-intestinal mucosal barrier and microbiota remains poorly understood. The present study was conducted with weaned piglets to address this issue. Postweaning piglets were fed for 4 weeks a corn- and soybean meal-based diet supplemented with 0 (Control), 0.1, 0.2, or 0.4% Trp. The small-intestinal microbiota and serum amino acids were analyzed by bacterial 16S rRNA gene-based high-throughput sequencing methods and high-performance liquid chromatography, respectively. The mRNA levels for genes involved in host defense and the abundances of tight-junction proteins in jejunum and duodenum were measured by real time-PCR and Western blot techniques, respectively. The concentrations of Trp in the serum of Trp-supplemented piglets increased in a dose-dependent manner. Compared with the control group, dietary supplementation with 0.2–0.4% Trp reduced the abundances of Clostridium sensu stricto and Streptococcus in the jejunum, increased the abundances of Lactobacillus and Clostridium XI (two species of bacteria that can metabolize Trp) in the jejunum, and augmented the concentrations of secretory immunoglobulin A (sIgA) as well as mRNA levels for porcine β-defensins 2 and 3 in jejunal tissues. Moreover, dietary Trp supplementation activated the mammalian target of rapamycin signaling and increased the abundances of tight-junction proteins (zonula occludens (ZO)-1, ZO-3, and claudin-1) in jejunum and duodenum. We suggested that Trp-metabolizing bacteria in the small intestine of weaned pigs primarily mediated the beneficial effects of dietary Trp on its mucosal integrity, health, and function.

Effects of dietary tryptophan supplementation in the acetic acid-induced colitis mouse model

Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract and is strongly associated with intestinal immunity and the microbiome. Tryptophan (Trp) is an inflammatory inhibitor and modulator of the intestinal microflora. We explored the serum profile of amino acids and the effects of diet supplementation with Trp (1.0 g kg-1) on intestinal immunity and microbiota in the acetic acid-induced colitis mouse model. We analyzed the survival rate, colonic morphological parameters, profiles of serum amino acids, microbiota in colonic contents and the relative gene abundance of intestinal proinflammatory cytokines. Although the dietary Trp supplementation failed to improve the survival rate and ameliorate the morphological parameters of colon in mice with colitis, Trp modulated the general serum amino acid profile by reducing the amino acid profiles of threonine, methionine and proline, affected intestinal immunity by inhibiting the colonic expression of interleukin-22 and changed the microbiota by reducing the abundance of Candidatus, Clostridium and Coprococcus at the genus level. In conclusion, dietary Trp supplementation in a mouse model of colitis did not ameliorate the survival rate and morphological parameters of colon but did modulate the serum amino acid profiles, intestinal immunity and microbiota. These findings enhance our understanding of the roles of Trp in the metabolism of serum amino acids, intestinal immunity and microbiota.

Dietary Supplementation with Lactobacillus casei Alleviates Lipopolysaccharide-Induced Liver Injury in a Porcine Model

This study aims to determine whether Lactobacillus casei (L. casei) could relieve liver injury in piglets challenged with lipopolysaccharide (LPS). Piglets were randomly allocated into one of the three groups: control, LPS, and L. casei. The control and LPS groups were fed a corn- and soybean meal-based diet, whereas the L. casei group was fed the basal diet supplemented with 6 × 10⁶ cfu/g L. casei. On Day 31 of the trial, piglets in the LPS and L. casei groups received intraperitoneal administration of LPS (100 µg/kg body weight), while the control group received the same volume of saline. Blood and liver samples were collected for analysis. Results showed that L. casei supplementation decreased the feed/gain ratio (p = 0.027) and diarrhea incidence (p < 0.001), and attenuated LPS-induced liver histomorphological abnormalities. Compared with the control group, LPS challenge dramatically increased glutamyl transpeptidase activity (p = 0.001) in plasma as well as the concentrations of Interleukin 6 (IL-6) (p = 0.048), Tumor necrosis factor-alpha (TNF-α) (p = 0.041), and Malondialdehyde (MDA) (p = 0.001) in the liver, while decreasing the hepatic SOD activity. LPS also increased (p < 0.05) the mRNA levels for IL-6, IL-8, TNF-α, Toll-like receptors 4 (TLR4), Nuclear factor κB (NF-κB) and Heat shock protein 70 (HSP70) in the liver. The adverse effects of LPS challenge were ameliorated by L. casei supplementation. In conclusion, dietary L. casei alleviates LPS-induced liver injury via reducing pro-inflammatory cytokines and increasing anti-oxidative capacity.

Increased expressions of genes and proteins involved in mitochondrial oxidation and antioxidant pathway in adipose tissue of pigs selected for a low residual feed intake

Adipose tissue is a primary sensor for nutrient availability and regulates many functions including feed intake and energy homeostasis. This study was undertaken to determine the molecular responses of adipose tissue to differences in feed intake and feed efficiency. Subcutaneous adipose tissue was collected from two lines of pigs divergently selected for residual feed intake (RFI), a measure of feed efficiency defined as the difference between actual and expected feed intake, and from a subset of high-RFI pigs that were feed-restricted at the level of the voluntary feed intake of low-RFI pigs during the growing-finishing period. Transcriptomics analyses indicated that the number of genes that were differentially expressed ( < 0.01) between low- and high-RFI pigs ( = 8 per group at each stage) in adipose tissue was much lower when pigs were considered at 19 kg (postweaning) than at 115 kg BW (market weight). Extended investigations were performed at 115 kg BW to compare low-RFI ( = 8), high-RFI ( = 8), and feed-restricted high-RFI ( = 8) pigs. They included in silico pathway analyses of the differentially expressed (DE) genes ( < 0.01) and a complementary proteomic investigation to list adipose proteins with a differential abundance ( < 0.10). Only 23% of the DE genes were affected by both RFI and feed restriction. This indicates that the responses of adipose tissue to RFI difference shared only some common mechanisms with feed intake modulation, notably the regulation of cell cycle (including ) and transferase activity pathway. Two carboxylesterase genes (, ) involved in lipolysis, were among the most overexpressed genes in the low-RFI pigs; they were also affected by feed restriction within the high-RFI line. About 60% of the molecular changes between low- and high-RFI pigs were specific to genetic divergence in feed efficiency, independently of feed intake. Different genes and proteins known to be associated with mitochondrial oxidative metabolism were overexpressed in adipose tissue of low-RFI pigs compared with high-RFI pigs; other proteins participating in the generation of energy were also affected by feed restriction within the high-RFI line. Finally, mitochondrial antioxidant genes were upregulated in low-RFI pigs vs. high-RFI pigs. Altogether, increased oxidative and antioxidant processes in adipose tissue might be associated with improved feed efficiency.

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

BACKGROUND

Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI).

RESULTS

Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines.

CONCLUSIONS

Non-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency.

N-Acetylcysteine supplementation alleviates intestinal injury in piglets infected by porcine epidemic diarrhea virus

Porcine epidemic diarrhea virus (PEDV) infects the intestine of young pigs, but effective measures for prevention and treatment are lacking. N-Acetylcysteine (NAC) has been shown to reduce endotoxin-induced intestinal dysfunction. This study was conducted with the PEDV-infected neonatal piglet model to determine the effect of NAC supplementation on intestinal function. Thirty-two 7-day-old piglets were randomly allocated to one of four treatments in a 2 × 2 factorial design consisting of two liquid diets (0 or 50 mg/kg BW NAC supplementation) and oral administration of 0 or 10^4.5 TCID₅₀ (50% tissue culture infectious dose) PEDV. On day 7 of the trial, half of the pigs (n = 8) in each dietary treatment received either sterile saline or PEDV (Yunnan province strain) solution at 10^4.5 TCID₅₀ per pig. On day 10 of the trial, D-xylose (0.1 g/kg BW) was orally administrated to all pigs. One hour later, jugular vein blood samples were collected, and then all pigs were killed to obtain the small intestine. PEDV infection increased diarrhea incidence, while reducing ADG. PEDV infection also decreased plasma D-xylose concentration, small intestinal villus height, mucosal I-FABP and villin mRNA levels but increased mucosal MX1 and GCNT3 mRNA levels (P < 0.05). Dietary NAC supplementation ameliorated the PEDV-induced abnormal changes in all the measured variables. Moreover, NAC reduced oxidative stress, as indicated by decreases in plasma and mucosal H₂O₂ levels. Collectively, these novel results indicate that dietary supplementation with NAC alleviates intestinal mucosal damage and improves the absorptive function of the small intestine in PEDV-infected piglets.

Effects of arginine supplementation during early gestation (day 1 to 30) on litter size and plasma metabolites in gilts and sows

Two experiments were conducted, under typical commercial swine production conditions, to determine effects of dietary arginine supplementation during early gestation on the performance of gilts and sows. In Exp. 1, between d 1 and 30 of gestation, 62 Landrace gilts and 113 sows consumed a corn- and soybean meal-based diet supplemented with 1.3% -arginine HCl or 2.2% -alanine. Total numbers of piglets born ( < 0.05) and born alive ( < 0.01) per litter and litter birth weights of piglets born ( < 0.05) and born alive ( < 0.05) were increased in the arginine group compared with the control. In Exp. 2, 155 multiparous Landrace sows received 1.3% -arginine HCl supplementation between d 1 and 14 (T2; = 41), d 15 and 30 (T3; = 40), or d 1 and 30 (T4; = 37), whereas the control group received 2.2% -alanine supplementation between d 1 and 30 (T1; = 37). Blood samples were randomly obtained from 6 sows per group on d 1, 14, and 28 of gestation to determine plasma concentrations of AA and related metabolites. Total numbers of piglets born ( = 0.084) and born alive ( = 0.080) per litter tended to be higher for sows supplemented with arginine between d 1 and 14 of gestation (T2) than for control sows (T1). Concentrations of arginine and nitric oxide metabolites were greater ( < 0.05) in T4 compared with T1 and T3 on d 14 of gestation and were also greater in T4 compared with T1 and T2 on d 28 of gestation. Plasma concentrations of spermidine ( < 0.001) were increased in T3 and T4 compared with T1 and T2 on d 28. These results indicate that dietary arginine supplementation during early gestation improves the reproductive performance of gilts and sows, possibly via nitric oxide and polyamine-dependent mechanisms.

Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location

BACKGROUND

Changing the energy and nutrient source for growing animals may be an effective way of limiting adipose tissue expansion, a response which may depend on the genetic background of the animals. This study aims to describe the transcriptional modulations present in the adipose tissues of two pig lines divergently selected for residual feed intake which were either fed a high-fat high-fiber (HF) diet or an isocaloric low-fat high-starch diet (LF).

RESULTS

Transcriptomic analysis using a porcine microarray was performed on 48 pigs (n = 12 per diet and per line) in both perirenal (PRAT) and subcutaneous (SCAT) adipose tissues. There was no interaction between diet and line on either adiposity or transcriptional profiles, so that the diet effect was inferred independently of the line. Irrespective of line, the relative weights of the two fat depots were lower in HF pigs than in LF pigs after 58 days on dietary treatment. In the two adipose tissues, the most apparent effect of the HF diet was the down-regulation of several genes associated with the ubiquitin-proteasome system, which therefore may be associated with dietary-induced modulations in genes acting in apoptotic and cell cycle regulatory pathways. Genes involved in glucose metabolic processes were also down-regulated by the HF diet, with no significant variation or decreased expression of important lipid-related genes such as the low-density lipoprotein receptor and leptin in the two fat pads. The master regulators of glucose and fatty acid homeostasis SREBF1 and MLXIPL, and peroxisome proliferator-activated receptor (PPAR)δ and its heterodimeric partner RXRA were down-regulated by the HF diet. PPARγ which has pleiotropic functions including lipid metabolism and adipocyte differentiation, was however up-regulated by this diet in PRAT and SCAT. Dietary-related modulations in the expression of genes associated with immunity and inflammation were mainly revealed in PRAT.

CONCLUSION

A high-fat high-fiber diet depressed glucose and lipid anabolic molecular pathways, thus counteracting adipose tissue expansion. Interaction effects between dietary intake of fiber and lipids on gene expression may modulate innate immunity and inflammation, a response which is of interest with regard to chronic inflammation and its adverse effects on health and performance.

Whole Blood Transcriptomics Is Relevant to Identify Molecular Changes in Response to Genetic Selection for Feed Efficiency and Nutritional Status in the Pig

The molecular mechanisms underlying feed efficiency need to be better understood to improve animal efficiency, a research priority to support a competitive and sustainable livestock production. This study was undertaken to determine whether pig blood transcriptome was affected by differences in feed efficiency and by ingested nutrients. Growing pigs from two lines divergently selected for residual feed intake (RFI) and fed isoproteic and isocaloric diets contrasted in energy source and nutrients were considered. Between 74 and 132 days of age, pigs (n = 12 by diet and by line) received a regular diet rich in cereals and low in fat (LF) or a diet where cereals where partially substituted by lipids and fibers (HF). At the end of the feeding trial, the total number of white blood cells was not affected by the line or by the diet, whereas the red blood cell number was higher (P<0.001) in low RFI than in high RFI pigs. Analysis of the whole blood transcriptome using a porcine microarray reveals a higher number of probes differentially expressed (DE) between RFI lines than between diets (2,154 versus 92 probes DE, P<0.01). This corresponds to 528 overexpressed genes and 477 underexpressed genes in low RFI pigs compared with high RFI pigs, respectively. Overexpressed genes were predominantly associated with translational elongation. Underexpressed genes were mainly involved in the immune response, regulation of inflammatory response, anti-apoptosis process, and cell organization. These findings suggest that selection for RFI has affected the immune status and defense mechanisms of pigs. Genes DE between diets were mainly related to the immune system and lipid metabolism. Altogether, this study demonstrates the usefulness of the blood transcriptome to identify the main biological processes affected by genetic selection and feeding strategies.

Whole-Blood Gene Expression Profiles in Large-Scale Epidemiological Studies: What Do They Tell?

In nutrigenomics, gene expression profiling is used to investigate transcriptional mechanisms associated with nutrients and diet. Blood samples collected in the framework of dietary interventions and epidemiological studies allow the use of humans as the model system, as opposed to using cell lines or animal models. Here, we review recent publications in the field of gene expression profiling, based on a systematic literature search focusing on studies from the last 5 years and including studies that investigated either single nutrients, foods, food groups, or dietary patterns. Findings highlight the role of inflammatory processes as key mediators of the association between diet and disease and point to the relevance of using blood as the target tissue in nutrigenomics. However, recurring challenges include study design issues, practical and statistical challenges, and biological interpretation of the results. Many of the published studies have small sample size, and given the nature of gene expression data, their conclusions have limited impact. These challenges should be addressed by future nutrigenomics studies in order to increase their relevance and validity.

L-Glutamine enhances enterocyte growth via activation of the mTOR signaling pathway independently of AMPK

Neonates (including human infants) require L-glutamine (Gln) for optimal intestinal health. This study tested the hypothesis that Gln enhances enterocyte growth via both mammalian target of rapamycin (mTOR) and AMP-activated kinase (AMPK) signaling pathways. Intestinal porcine epithelial cells (IPEC-1) were cultured for 3 days in Gln-free Dulbecco's modified Eagle medium containing 0 or 2 mM Gln. To determine the role of mTOR and AMPK on cell growth, additional experiments were conducted where medium contained 2 mM Gln and 10 nM rapamycin (Rap, an inhibitor of mTOR) or 1 μM compound C (an inhibitor of AMPK). IPEC-1 cell growth increased with increasing concentrations of Gln from 0 to 2 mM. Compared with 0 mM Gln, 2 mM Gln increased (P < 0.05) the amounts of phosphorylated 4E-binding protein 1 (4E-BP1) and ribosomal protein S6 kinase (p70S6 kinase) proteins but did not affect abundances of total or phosphorylated AMPK protein. Gln also increased mRNA levels for Bcl-2, mTOR, p70S6 kinase, 4E-BP1, COX7C, ASCT2, ODC, SGLT-1, CFTR, Na(+)/K(+)-ATPase, HSP70, and ZO-1. Similarly, cells cultured with Rap and Gln exhibited higher (P < 0.05) abundances of phosphorylated 4E-BP1 and p70S6 kinase proteins than the Rap-only group, whereas abundances of phosphorylated mTOR and 4E-BP1 proteins were increased when AMPK was inhibited by compound C. Conversely, the amount of phosphorylated AMPK increased when mTOR was inhibited by Rap, suggesting a negative cross-talk between mTOR and AMPK. Collectively, these results indicate that Gln stimulates enterocyte growth by activating the mTOR signaling pathway independently of AMPK.

Putrescine stimulates the mTOR signaling pathway and protein synthesis in porcine trophectoderm cells

Insufficient placental growth is a major factor contributing to intrauterine growth retardation in mammals. There is growing evidence that putrescine produced from arginine (Arg) and proline via ornithine decarboxylase is a key regulator of angiogenesis, embryogenesis, as well as placental and fetal growth. However, the underlying mechanisms are largely unknown. The present study tested the hypothesis that putrescine stimulates protein synthesis by activating the mechanistic target of rapamycin (mTOR) signaling pathway in porcine trophectoderm cell line 2 cells. The cells were cultured for 2 to 4 days in customized Arg-free Dulbecco modified Eagle Ham medium containing 0, 10, 25, or 50 μM putrescine or 100 μM Arg. Cell proliferation, protein synthesis, and degradation, as well as the abundance of total and phosphorylated mTOR, ribosomal protein S6 kinase 1, and eukaryotic initiation factor 4E-binding protein-1 (4EBP1), were determined. Our results indicate that putrescine promotes cell proliferation and protein synthesis in a dose- and time-dependent manner, which was inhibited by difluoro-methylornithine (an inhibitor of ornithine decarboxylase). Moreover, supplementation of culture medium with putrescine increased the abundance of phosphorylated mTOR and its downstream targets, 4EBP1 and p70 S6K1 proteins. Collectively, these findings reveal a novel and important role for putrescine in regulating the mTOR signaling pathway in porcine placental cells. We suggest that dietary supplementation with or intravenous administration of putrescine may provide a new and effective strategy to improve survival and growth of embryos/fetuses in mammals.

Omics and integrated omics for the promotion of food and nutrition science

Transcriptomics, proteomics, and metabolomics are three major platforms of comprehensive omics analysis in the science of food and complementary medicine. Other omics disciplines, including those of epigenetics and microRNA, are matters of increasing concern. The increased use of the omics approach in food science owes much to the recent advancement of technology and bioinformatic methodologies. Moreover, many researchers now put the combination of multiple omics analysis (integrated omics) into practice to exhaustively understand the functionality of food components. However, data analysis of integrated omics requires huge amount of work and high skill of data handling. A database of nutritional omics data was constructed by the authors, which should help food scientists to analyze their own omics data more effectively. In addition, a novel tool for the easy visualization of omics data was developed by the authors’ group. The tool enables one to overview the changes of multiple omics in the KEGG pathway. Research in traditional and complementary medicine will be further facilitated by promoting the integrated omics research of food functionality. Such integrated research will only be possible with the effective collaboration of scientists with different backgrounds.

Metabolomic analysis of amino acid and energy metabolism in rats supplemented with chlorogenic acid

This study was conducted to investigate effects of chlorogenic acid (CGA) supplementation on serum and hepatic metabolomes in rats. Rats received daily intragastric administration of either CGA (60 mg/kg body weight) or distilled water (control) for 4 weeks. Growth performance, serum biochemical profiles, and hepatic morphology were measured. Additionally, serum and liver tissue extracts were analyzed for metabolomes by high-resolution (1)H nuclear magnetic resonance-based metabolomics and multivariate statistics. CGA did not affect rat growth performance, serum biochemical profiles, or hepatic morphology. However, supplementation with CGA decreased serum concentrations of lactate, pyruvate, succinate, citrate, β-hydroxybutyrate and acetoacetate, while increasing serum concentrations of glycine and hepatic concentrations of glutathione. These results suggest that CGA supplementation results in perturbation of energy and amino acid metabolism in rats. We suggest that glycine and glutathione in serum may be useful biomarkers for biological properties of CGA on nitrogen metabolism in vivo.

Glycine is a nutritionally essential amino acid for maximal growth of milk-fed young pigs

Analysis of amino acids in milk protein reveals a relatively low content of glycine. This study was conducted with young pigs to test the hypothesis that milk-fed neonates require dietary glycine supplementation for maximal growth. Fourteen-day-old piglets were allotted randomly into one of four treatments (15 piglets/treatment), representing supplementation with 0, 0.5, 1 or 2% glycine (dry matter basis) to a liquid milk replacer. Food was provided to piglets every 8 h (3 times/day) for 2 weeks. Milk intake (32.0-32.5 g dry matter/kg body weight per day) did not differ between control and glycine-supplemented piglets. Compared with control piglets, dietary supplementation with 0.5, 1 and 2% glycine increased (P < 0.05) plasma concentrations of glycine and serine, daily weight gain, and body weight without affecting body composition, while reducing plasma concentrations of ammonia, urea, and glutamine, in a dose-dependent manner. Dietary supplementation with 0.5, 1 and 2% glycine enhanced (P < 0.05) small-intestinal villus height, glycine transport (measured using Ussing chambers), mRNA levels for GLYT1, and anti-oxidative capacity (indicated by increased concentrations of reduced glutathione and a decreased ratio of oxidized glutathione to reduced glutathione). These novel results indicate, for the first time, that glycine is a nutritionally essential amino acid for maximal protein accretion in milk-fed piglets. The findings not only enhance understanding of protein nutrition, but also have important implications for designing improved formulas to feed human infants, particularly low birth weight and preterm infants.

Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks

Background

Epidemiological studies in the recent years have investigated the relationship between dietary habits and disease risk demonstrating that diet has a direct effect on public health. Especially plant-based diets -fruits, vegetables and herbs- are known as a source of molecules with pharmacological properties for treatment of several malignancies. Unquestionably, for developing specific intervention strategies to reduce cancer risk there is a need for a more extensive and holistic examination of the dietary components for exploring the mechanisms of action and understanding the nutrient-nutrient interactions. Here, we used colon cancer as a proof-of-concept for understanding key regulatory sites of diet on the disease pathway.

Results

We started from a unique vantage point by having a database of 158 plants positively associated to colon cancer reduction and their molecular composition (~3,500 unique compounds). We generated a comprehensive picture of the interaction profile of these edible and non-edible plants with a predefined candidate colon cancer target space consisting of ~1,900 proteins. This knowledge allowed us to study systematically the key components in colon cancer that are targeted synergistically by phytochemicals and identify statistically significant and highly correlated protein networks that could be perturbed by dietary habits.

Conclusion

We propose here a framework for interrogating the critical targets in colon cancer processes and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. Our methodology for better delineating prevention of colon cancer by nutritional interventions relies heavily on the availability of information about the small molecule constituents of our diet and it can be expanded to any other disease class that previous evidence has linked to lifestyle.

Dietary supplementation with tributyrin alleviates intestinal injury in piglets challenged with intrarectal administration of acetic acid

Tributyrin (TBU) is a good dietary source of butyrate and has beneficial effects on the maintenance of normal intestinal morphology. The present study tested the hypothesis that dietary TBU supplementation could alleviate intestinal injury in the acetic acid (ACA)-induced porcine model of colitis. A total of eighteen piglets (25 d old) were randomly allocated to one of three treatment groups (control, ACA and TBU). The control and ACA groups were fed a basal diet and the TBU group was fed the basal diet supplemented with 0·1 % TBU. On day 15 of the trial, under anaesthesia, a soft catheter was inserted into the rectum of piglets (20-25 cm from the anus), followed by administration of either saline (control group) or ACA (10 ml of 10 % ACA solution for ACA and TBU groups). On day 22 of the trial, after venous blood samples were collected, piglets were killed to obtain mid-ileum and mid-colon mucosae. Compared with the control group, the ACA group exhibited an increase (P< 0·05) in lymphocyte counts, creatinine, PGE2, and malondialdehyde concentrations and diamine oxidase and inducible NO synthase activities in the plasma and lymphocyte density in the colon and a decrease in insulin concentrations and glutathione peroxidase activity, ileal villus height:crypt depth ratios and goblet cell numbers in the colon. These adverse effects of ACA were attenuated by TBU supplementation. Moreover, TBU prevented the ACA-induced increase in caspase-3 levels while enhancing claudin-1 protein and epidermal growth factor receptor (EGFR) mRNA expression in the colonic mucosa. Collectively, these results indicate that dietary supplementation with 0·1 % TBU alleviates ACA-induced intestinal injury possibly by inhibiting apoptosis, promoting tight-junction formation and activating EGFR signalling.

Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life

Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum's one gene-one polypeptide hypothesis, thereby reducing biological processes to single reactions or pathways. Systems thinking is needed to understand the complexity of health and disease processes requiring measurements of physiological processes, as well as environmental and social factors, which may alter the expression of genetic information. Analysis of physiological processes with omics technologies to assess systems' responses has only become available over the past decade and remains costly. Studies of environmental and social conditions known to alter health are often not connected to biomedical research. While these facts are widely accepted, developing and conducting comprehensive research programs for health are often beyond financial and human resources of single research groups. We propose a new research program on essential nutrients for optimal underpinning of growth and health (ENOUGH) that will use systems approaches with more comprehensive measurements and biostatistical analysis of the many biological and environmental factors that influence undernutrition. Creating a knowledge base for nutrition and health is a necessary first step toward developing solutions targeted to different populations in diverse social and physical environments for the two billion undernourished people in developed and developing economies.