Article

Nutrigenomics in livestock: systems biology meets nutrition

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Abstract

The advent of high-throughput technologies to study an animal’s genome, proteome, and metabolome (i.e., ‘omics’ tools) constituted a setback to the use of reductionism in livestock research. More recent development of ‘next-generation sequencing’ tools was instrumental in allowing in-depth studies of the microbiome in the rumen and other sections of the gastrointestinal tract. Omics, along with bioinformatics, constitutes the foundation of modern systems biology, a field of study widely-used in model organisms (e.g., rodents, yeast, humans) to enhance understanding of the complex biological interactions occurring within cells and tissues at the gene, protein, and metabolite level. Application of systems biology concepts is ideal for the study of interactions between nutrition and physiological state with tissue and cell metabolism and function during key life stages of livestock species, including the transition from pregnancy to lactation, in utero development, or post-natal growth. Modern bioinformatic tools capable of discerning functional outcomes and biologically-meaningful networks complement the ever increasing ability to generate large molecular, microbial, and metabolite datasets. Simultaneous visualization of the complex inter-tissue adaptations to physiological state and nutrition can now be discerned. Studies to understand the linkages between the microbiome and the absorptive epithelium using the integrative approach are emerging. We present examples of new knowledge generated through the application of functional analyses of transcriptomic, proteomic, and metabolomic datasets encompassing nutritional management of dairy cows, pigs, and poultry. Published work to date underscores that the integrative approach across and within tissues may prove useful for fine-tuning nutritional management of livestock. An important goal during this process is to uncover key molecular players involved in the organismal adaptations to nutrition.

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... In addition, the H. Allen Tucker Lactation and Endocrinology Award was presented to Dr. Steven Zinn of the University of Connecticut (Storrs). This issue contains papers based on 4 of the presentations given at the symposium Loor et al., 2015;McNamara, 2015;Moyes, 2015), which are subsequently introduced, and a short perspective on graduate education and mentoring in animal science from the Tucker Award winner (Zinn, 2015). ...
... Later in the day, Juan Loor (University of Illinois, Urbana) gave a presentation on using the systems biology toolbox consisting of the use of omics technology and bioinformatics together with performance and metabolic measurements to study nutrition in livestock species. Loor et al. (2015) gave a description of systems biology as it pertains to livestock nutrition and the technologies used (omics such as transcriptomics, proteomics, metabolomics, and microbiome), the workflows, and data analysis and data integration. Examples were given of application of the systems approach in the context of the peripartal cow, swine nutrition, and poultry nutrition as well as rumen-specific systems biology approaches looking at ruminal microbiome-epithelial interactions. ...
... Examples were given of application of the systems approach in the context of the peripartal cow, swine nutrition, and poultry nutrition as well as rumen-specific systems biology approaches looking at ruminal microbiome-epithelial interactions. Loor et al. (2015) further clarified that epigenetics is part of the systems approach and introduced the Functional Annotation of Animal Genomes (FAANG) project that aims to accelerate genome-to-phenome associations (Andersson et al., 2015). Loor et al. (2015) concluded by advocating for the holistic understanding of the animal's response to diet through systems biology approaches and reiterated the need for training and exposure of scientists in the field to the concept of systems biology. ...
... In previous studies, it has been reported that zinc deficiency hinders specific components of the immune system and the expression levels of antioxidant enzymes, but there is no strong evidence on the effect of extra zinc supplementation on the immune system and antioxidant enzymes (Feng et al., 2011). Given that nutrigenomic researches conceptualize the relationship between genes and nutrients from basic biology and should not be described from limited list of DEGs (Loor and Bionaz, 2015), hence, the effect of zinc dietary on the immune-related and metal ion binding pathways should be considered with the feasible consequences of zinc sources on the other biological systems. ...
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... Ainsi, une fois connue, la composition du microbiote ruminal individuelle peut être confrontée aux caractéristiques et aux performances de chaque animal qui l'héberge, ce qui permettrait à terme de perfectionner l'alimentation de précision et d'aider à répondre au mieux à la demande mondiale croissante en protéine animale (FEFAC, 2016b). Le développement des technologies de séquençage à haut débit du microbiote, permettant de connaître avec précision sa composition, est une condition essentielle pour parvenir à une alimentation sur mesure des animaux (Pitta et al., 2014;Loor et al., 2015). La prise en compte des besoins de certaines bactéries d'intérêt ou la maîtrise de la composition de la communauté microbienne ruminale peuvent également être des objectifs pour les fabricants d'aliment. ...
Thesis
Une meilleure compréhension de l’interrelation entre l’animal hôte et son microbiote ruminal pourrait être une première étape afin d’optimiser l’équilibre entre la valorisation des fibres par les ruminants et leur production de méthane. Deux axes ont été étudiés au court de cette thèse : (1) la résilience structurelle du microbiote après une perturbation de l’écosystème ruminal en fonction de la source énergétique alimentaire et (2) la spécificité du microbiote liée à l’animal hôte via l’étude des effets des flux d’entrée et de sortie de matière dans le rumen (spécifiques de l’hôte) sur la composition du microbiote. Une procédure innovante de synchronisation consistant à vider, mélanger et réintroduire le contenu des rumens dans chaque animal permet de créer une perturbation de l’écosystème ruminal et de fournir un même microbiote à tous les animaux. Cette procédure a été utilisée dans trois expérimentations sur 12 chèvres taries, sur 10 chèvres en lactation et sur 6 vaches taries. Les bactéries et les archées ont été suivies par séquençage de l’ADN codant pour l’ARNr 16S. Les microbiotes ont évolué vers une composition différente de celle avant synchronisation pour les 2 espèces nourries avec une ration riche en fibres. En revanche, avec des rations riches en glucides fermentescibles et en amidon, les microbiotes des deux espèces sont revenus à des compositions proches de la situation avant synchronisation. La source énergétique de la ration influence la résilience structurelle du microbiote. La spécificité du microbiote liée à l’hôte vient en partie du contrôle par l’animal des flux de matière organique entrant et sortant du rumen.
... In general, nutritional and genetics approaches, both in applied and scientific fields, have followed separate paths, ignoring how genome-nutrition interactions affect physiological and metabolic processes with important phenotypic consequences. From a metabolic perspective, quantitative and qualitative properties of the diet components have important regulatory effects on muscle and lipid metabolism and influence gene expression [2]. In this context, nutrigenomic studies make up a research field within nutritional sciences that allow us to elucidate how dietary nutrients can interact with genes affecting transcription factors, RNA and protein expression, cellular homeostasis, and metabolite production [3]. ...
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... Further, Zn level in the present study (97 mg/kg DM) was less than the maximum tolerable limit for sheep (750 mg/kg DM; NRC, 2007), and the animals showed no signs of illness, thus no Zn toxicity could be claimed. It is also worth mentioning that the results of nutrigenomics studies should be interpreted from a 'systems biology' and not from a limited list of DEGs point of view (Loor and Bionaz, 2015). Therefore, the effect of Zn supplementation on the cardiovascular system-related pathways presented herein should be viewed with the possible effects of Zn on the other systems. ...
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Validating statistical analysis methods for RNA sequencing (RNA-seq) experiments is a complex task. Researchers often find themselves having to decide between competing models or assessing the reliability of results obtained with a designated analysis program. Computer simulation has been the most frequently used procedure to verify the adequacy of a model. However, datasets generated by simulations depend on the parameterization and the assumptions of the selected model. Moreover, such datasets may constitute a partial representation of reality as the complexity or RNA-seq data is hard to mimic. We present the use of plasmode datasets to complement the evaluation of statistical models for RNA-seq data. A plasmode is a dataset obtained from experimental data but for which come truth is known. Using a set of simulated scenarios of technical and biological replicates, and public available datasets, we illustrate how to design algorithms to construct plasmodes under different experimental conditions. We contrast results from two types of methods for RNA-seq: (1) models based on negative binomial distribution (edgeR and DESeq), and (2) Gaussian models applied after transformation of data (MAANOVA). Results emphasize the fact that deciding what method to use may be experiment-specific due to the unknown distributions of expression levels. Plasmodes may contribute to choose which method to apply by using a similar pre-existing dataset. The promising results obtained from this approach, emphasize the need of promoting and improving systematic data sharing across the research community to facilitate plasmode building. Although we illustrate the use of plasmode for comparing differential expression analysis models, the flexibility of plasmode construction allows comparing upstream analysis, as normalization procedures or alignment pipelines, as well.
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The effects of anethole on in vitro and in vivo parameters of chicken immunity during experimental avian coccidiosis were evaluated. Anethole reduced the viability of invasive Eimeria acervulina sporozoites after 2 or 4 h of treatment in vitro by 45 and 42%, respectively, and stimulated 6.0-fold greater chicken spleen cell proliferation compared with controls. Broiler chickens continuously fed from hatch with an anethole-supplemented diet and orally challenged with live E. acervulina oocysts showed enhanced BW gain, decreased fecal oocyst excretion, and greater E. acervulina profilin antibody responses compared with infected chickens given an unsupplemented standard diet. The levels of transcripts encoding the immune mediators IL6, IL8, IL10, and tumor necrosis factor ligand superfamily member 15 (TNFSF15) in intestinal lymphocytes were increased in E. acervulina-infected chickens fed the anethole-containing diet compared with untreated controls. Global gene expression analysis by microarray hybridization identified 1,810 transcripts (677 upregulated, 1,133 downregulated) whose levels were significantly altered in intestinal lymphocytes of anethole-fed birds compared with unsupplemented controls. From this transcriptome, 576 corresponding genes were identified. The most significant biological function associated with these genes was “Inflammatory Response” in the “Disease and Disorders” category. This new information documents the immunologic and genomic changes that occur in chickens following anethole dietary supplementation that may be relevant to host protective immune response to avian coccidiosis.
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It was recently shown that variations in the ratio of dietary fermentable carbohydrates (fCHO) and fermentable protein (fCP) differentially affect large intestinal microbial ecology and the mucosal response. Here we investigated the use of mass spectrometry to profile changes in metabolite composition in colon and urine associated with variation in dietary fCHO and fCP composition and mucosal physiology. Thirty-two weaned pigletswere fed 4 diets in a 2 x 2 factorial design with low fCP and low fCHO, low fCP and high fCHO, high fCP and low fCHO, and high fCP and high fCHO. After 21 to 23 d, all pigs were euthanized and colon digesta and urine metabolite profiles were obtained by mass spectrometry. Analysis of mass spectra by partial least squares approach indicated a clustering of both colonic and urinary profiles for each pig by feeding group. Metabolite identification and annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed increased abundance of metabolites associated with arachidonic acid metabolism in colon of pigs fed a high concentration of fCP irrespective of dietary fCHO. Urinary metabolites did not show as clear patterns. Mass spectrometry can effectively differentiate metabolite profiles in colon contents and urine associated with changes in dietary composition. Whether metabolite profiling is an effective tool to identify specific metabolites (biomarkers) or metabolite profiles associated with gut function and integrity needs further elucidation.
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Maternal nutrition exclusively during the periconceptional period can induce remarkable effects on both oocyte maturation and early embryo development, which in turn can have lifelong consequences. The objective of this study was to evaluate the effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos. Holstein cows were randomly assigned to one of two treatments differing in level of dietary methionine (1.89 Met vs. 2.43 Met % of metabolizable protein) from calving until embryo flushing. High quality preimplantation embryos from individual cows were pooled and then analyzed by RNA sequencing. Remarkably, a subtle difference in methionine supplementation in maternal diet was sufficient to cause significant changes in the transcriptome of the embryos. A total of 276 genes out of 10,662 showed differential expression between treatments (FDR <0.10). Interestingly, several of the most significant genes are related to embryonic development (e.g., VIM, IFI6, BCL2A1, and TBX15) and immune response (e.g., NKG7, TYROBP, SLAMF7, LCP1, and BLA-DQB). Likewise, gene set enrichment analysis revealed that several Gene Ontology terms, InterPro entries, and KEGG pathways were enriched (FDR <0.05) with differentially expressed genes involved in embryo development and immune system. The expression of most genes was decreased by maternal methionine supplementation, consistent with reduced transcription of genes with increased methylation of specific genes by increased methionine. Overall, our findings provide evidence that supplementing methionine to dams prior to conception and during the preimplantation period can modulate gene expression in bovine blastocysts. The ramifications of the observed gene expression changes for subsequent development of the pregnancy and physiology of the offspring warrant further investigation in future studies.
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Intramuscular fat (IMF) content is positively correlated with aspects of pork palatability, including flavour, juiciness and overall acceptability. The ratio of energy to protein in the finishing diet of growing pigs can impact on IMF content with consequences for pork quality. The objective of this study was to compare gene expression profiles of Musculus semimembranosus (SM) of animals divergent for IMF as a consequence of protein dietary restriction in an isocaloric diet. The animal model was derived through the imposition of low or high protein diets during the finisher stage in Duroc gilts. RNA was extracted from post mortem SM tissue, processed and hybridised to Affymetrix porcine GeneChip(R) arrays. IMF content of SM muscle was increased on the low protein diet (3.60 +/- 0.38% versus 1.92 +/- 0.35%). Backfat depth was also greater in animals on the low protein diet, and average daily gain and feed conversion ratio were lower, but muscle depth, protein content and moisture content were not affected. A total of 542 annotated genes were differentially expressed (DE) between animals on low and high protein diets, with 351 down-regulated and 191 up-regulated on the low protein diet. Transcript differences were validated for a subset of DE genes by qPCR. Alterations in functions related to cell cycle, muscle growth, extracellular matrix organisation, collagen development, lipogenesis and lipolysis, were observed. Expression of adipokines including LEP, TNFalpha and HIF1alpha were increased and the hypoxic stress response was induced. Many of the identified transcriptomic responses have also been observed in genetic and fetal programming models of differential IMF accumulation, indicating they may be robust biological indicators of IMF content. An extensive perturbation of overall energy metabolism in muscle occurs in response to protein restriction. A low protein diet can modulate IMF content of the SM by altering gene pathways involved in lipid biosynthesis and degradation; however this nutritional challenge negatively impacts protein synthesis pathways, with potential consequences for growth.
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A major challenge of the post-genomics era is to define the connectivity of protein phosphorylation networks. Here, we quantitatively delineate the insulin signaling network in adipocytes by high-resolution mass spectrometry-based proteomics. These data reveal the complexity of intracellular protein phosphorylation. We identified 37,248 phosphorylation sites on 5,705 proteins in this single-cell type, with approximately 15% responding to insulin. We integrated these large-scale phosphoproteomics data using a machine learning approach to predict physiological substrates of several diverse insulin-regulated kinases. This led to the identification of an Akt substrate, SIN1, a core component of the mTORC2 complex. The phosphorylation of SIN1 by Akt was found to regulate mTORC2 activity in response to growth factors, revealing topological insights into the Akt/mTOR signaling network. The dynamic phosphoproteome described here contains numerous phosphorylation sites on proteins involved in diverse molecular functions and should serve as a useful functional resource for cell biologists.
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High-producing dairy cows experience a sudden and significant increase in energy requirements due to the onset of milk production in early lactation. They mobilize body reserves, mainly adipose tissue, resulting in an increased risk of production decline and the development of health disorders. The objective of the present study was to investigate the effects of feeding oilseeds (rapeseed) during the dry period, thereby priming dairy cows for metabolism of body fat in early lactation. Forty-three Holstein dairy cows were used, 14 were primiparous and 29 were multiparous (≥2nd lactation). In the dry period, 8 wk before expected calving until calving, the cows were fed either a diet with a high content of rapeseed in the total mixed ration (HF) or a standard total mixed ration with a low content of fat (CON). During the first 5 wk after calving, all the cows were fed a standard low fat lactation ration. The treatments were evaluated by performance and metabolic variables in blood and liver. The dry period diet had no effects on body weight and body condition score of the cows during the dry period and in early lactation. The daily yield of milk, protein, and lactose did not differ among treatments. However, the milk fat concentration was lower and the daily milk fat production tended to be lower for the cows fed the HF diet in the dry period compared with the cows fed the CON diet. The plasma content of nonesterified fatty acids, cholesterol, and phospholipids in the dry period was increased in the HF dry period diet compared with the CON diet. The lower plasma concentration of uric acid obtained prepartum for the cows fed the HF diet may indicate a lower rumen microbial protein synthesis. Postpartum, the plasma concentration of β-hydroxybutyric acid tended to be lower for the cows fed the HF dry period diet. The liver content of triglycerides was lower and the liver content of glycogen was higher in early lactation among the cows fed the HF dry period diet compared with the cows fed the CON diet. Based on liver glycogen, triglyceride content, and blood β-hydroxybutyric acid concentration, it could be argued that intake of oilseeds during the dry period is a positive strategy for priming dairy cows for fat metabolism in the following early lactation.
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Understanding the basis for differences in nutrient requirements and for nutrient effects on health and performance requires an appreciation of the links between nutrition and gene expression. We developed and applied molecular probes to characterize diet-associated postabsorptive hepatic gene expression in growing pigs chronically fed protein-restricted diets based on either casein (CAS) or soy protein isolate (SPI). Eighty-eight expressed sequence tags (ESTs) were identified on the basis of diet-related changes in expression, by using an mRNA differential display method. Expression profiling based on transcription analysis by real-time reverse transcriptase- polymerase chain reaction showed that the SPI diet significantly changed the pattern of gene expression as compared with the CAS diet and allowed identification of coregulated genes. The expression of six genes involved in the metabolism of stress response (glutathione S-transferase, peptide methionine sulfoxide reductase, apolipoprotein A-I, organic anion transport polypeptide 2, calnexin, heat shock transcription factor 1) exhibited significant changes in the transcription level and indicated an increased oxidative stress response in pigs fed the SPI diet. Hierarchical clustering of gene expression data of all 33 ESTs analyzed across 14 pigs fed the two different diets resulted in clustering of genes related to the oxidative stress response with genes related to the regulation of gene expression and neuronal signaling.
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Seventy-two pigs at 34.4kg body weight (BW) were allotted to two treatments with six replicates/treatment and six pigs/pen: the CON (negative control, no added selenium (Se)) and the OS (0.36mg/kg added selenium from selenium-enriched yeast). Pigs were fed until 130kg BW. The CON diet contained 0.18mg/kg indigenous Se whereas the OS diet contained 0.54mg/kg Se. Blood samples were collected at 130kg BW and further processed for microarray analysis, prepared with 885 genes related to immune function of pigs. Among those, 28 genes related to improved immune status and innate immunity were up-regulated (P<0.05) in leukocytes from Se-fed pigs and those include major histocompatibility class I (>1.66), arginase I (>1.27), integrin beta-1-subunit (>1.20), toll like receptor 2 (>1.12) and double-stranded RNA-dependent protein kinase. However, 24 genes including tissue factor (<4.70), serum amyloid A-2 protein (<3.11) and p27Kip1 (<1.42) were down-regulated (P<0.05) in leukocytes from Se-fed pigs. Expression of four selected genes was validated using quantitative PCR (qPCR) showing significant correlation between mircroarray analysis and qPCR analysis. This study indicates that a long- term dietary supplementation (0.3%) of organic Se improves the expression of genes that are related to enhanced immunity of pigs.
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The bacterial diversity of the bovine rumen was examined using a PCR-based approach. 16S rDNA sequences were amplified and cloned from three fractions of rumen (solid, fluid, and epithelium) that are likely to represent different bacterial niches. A total of 113 clones were sequenced, and similarities to known 16S rDNA sequences were examined. About 47.8% of the sequences had 90-97% similarity to 16S rDNA database sequences. Furthermore, about 62.2% of the sequences were 98-100% similar to 16S rDNA database sequences. For the remaining 6.1%, the similarity was less than 90%. Phylogenetic analysis was also used to infer the makeup of the bacterial communities in the different rumen fractions. The Cytophaga-Flexibacter-Bacteroides group (CFB, 67.5%), low G+C Gram-positive bacteria (LGCGPB, 30%), and Proteobacteria (2.5%) were represented in the rumen fluid clone set; LGCGPB (75.7%), CFB (10.8%), Proteobacteria (5.4%), high G+C Gram-positive bacteria (HGCGPB, 5.4%), and Spirochaetes (2.7%) were represented in the rumen solid clone set; and the CFB group (94.4%) and LGCGPB (5.6%) were represented in the rumen epithelium clone set. These findings suggest that the rumen fluid, solid, and epithelium support different microbial populations that may play specific roles in rumen function.
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This experiment was to determine if replacing soybean meal with fermented soybean meal (FSBM) would reduce the innate immune response after lipopolysaccharide challenge and the changes of gene expression profiles associated with this response. Forty-eight 21 day-old pigs were housed individually and fed three diets for 15 days: CON (a diet without FSBM or spray-dried plasma protein; SDPP), PP7 (a diet with 7% SDPP), and FS10 (a diet with 10% FSBM). Pigs were fitted with a jugular vein catheters receiving lipopolysaccharide challenge (25 μg/kg body weight (BW)) on day 15. Blood was collected for 5 h at 30-min intervals to measure cortisol. Expressions of gene transcripts in total RNA from leukocytes were compared using an oligonucleotide microarray at 210 min after lipopolysaccharides injection. Cortisol of FS10 was lower (P < 0.05) than CON after lipopolysaccharides challenge. The expression levels of 17 transcripts, including cytosolic glutathione peroxidase and glutathione S-transferase A4-4 were increased (P < 0.05), whereas 23 genes including adiponectin, neonatal Fc receptor and tumor necrosis factor ligand superfamily member 5 were decreased (P < 0.05) in FS10. This study suggests that FSBM-fed pigs can modulate expression of genes related to inflammatory response and anti-oxidant activity which can be a potential reason for reduced serum cortisol. © 2014 Japanese Society of Animal Science.
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Background: Maternal nutrition during different stages of pregnancy can induce significant changes in the structure, physiology, and metabolism of the offspring. These changes could have important implications on food animal production especially if these perturbations impact muscle and adipose tissue development. Here, we evaluated the impact of different maternal isoenergetic diets, alfalfa haylage (HY; fiber), corn (CN; starch), and dried corn distillers grains (DG; fiber plus protein plus fat), on the transcriptome of fetal muscle and adipose tissues in sheep. Results: Prepartum diets were associated with notable gene expression changes in fetal tissues. In longissimus dorsi muscle, a total of 224 and 823 genes showed differential expression (FDR < 0.05) in fetuses derived from DG vs. CN and HY vs. CN maternal diets, respectively. Several of these significant genes affected myogenesis and muscle differentiation. In subcutaneous and perirenal adipose tissues, 745 and 208 genes were differentially expressed (FDR < 0.05), respectively, between CN and DG diets. Many of these genes are involved in adipogenesis, lipogenesis, and adipose tissue development. Pathway analysis revealed that several GO terms and KEGG pathways were enriched (FDR < 0.05) with differentially expressed genes associated with tissue and organ development, chromatin biology, and different metabolic processes. Conclusions: These findings provide evidence that maternal nutrition during pregnancy can alter the programming of fetal muscle and fat tissues in sheep. The ramifications of the observed gene expression changes, in terms of postnatal growth, body composition, and meat quality of the offspring, warrant future investigation.
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In our modern ‘omics era, metabolic flux analysis (fluxomics) represents the physiological counterpart of its siblings transcriptomics, proteomics and metabolomics. Fluxomics integrates in vivo measurements of metabolic fluxes with stoichiometric network models to allow the determination of absolute flux through large networks of the central carbon metabolism. There are many approaches to implement fluxomics including flux balance analysis (FBA), 13C fluxomics and 13C-constrained FBA as well as many experimental settings for flux measurement including dynamic, stationary and semi-stationary. Here we outline the principles of the different approaches and their relative advantages. We demonstrate the unique contribution of flux analysis for phenotype elucidation using a thoroughly studied metabolic reaction as a case study, the microbial aerobic/anaerobic shift, highlighting the importance of flux analysis as a single layer of data as well as interlaced in multi-omics studies.
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Adipose tissue is not only a tissue where energy is stored but is also involved in regulating several body functions such as appetite and energy expenditure via its endocrine activity. Moreover, it thereby modulates complex processes like reproduction, inflammation and immune response. The products secreted from adipose tissue comprise hormones and cytokines that are collectively termed as adipocytokines or "adipokines"; the discovery and characterization of new proteins secreted by adipose tissue is still ongoing and their number is thus still increasing. Adipokines act in both endocrine manner as well as locally as autocrine or paracrine effectors. Proteomics has emerged as a valuable technique to characterize both cellular and secreted proteomes from adipose tissues, including those of main cellular fractions, i.e. the adipocytes or the stromal vascular fraction containing mainly adipocyte precursors and immune cells. The increased scientific interest in adipose tissue is largely based on the worldwide increasing prevalence of obesity in humans; in contrast, obesity is hardly an issue for farmed animals that are fed according to their well-defined needs. Adipose tissue is nevertheless of major importance in these animals, as the adipose percentage of the bodyweight is a major determinant for the efficiency of transferring nutrients from feed into food products and thus of the economic value from meat producing animals. In dairy animals, the importance of adipose tissue is based on its function as stromal structure for the mammary gland and on its role in participating in and regulating of energy metabolism and other functions. Moreover, as pig has recently become an important model organism the study of human diseases, the knowledge of adipose tissue metabolism in pig is relevant for the study of human obesity and metabolic disorders. We herein provide a general overview of adipose tissue functions, and of its importance in farm animals. This review will summarize recent achievements in farm animal adipose tissue proteomics, mainly in cattle and pigs, but also in poultry, i.e. chicken and in farmed fish. Proteomics advancement in adipocyte cell lines, have also been included.
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This study was aimed to investigate the impact of subacute ruminal acidosis (SARA) on the diversity of liquid (LAB) and solid-associated bacteria (SAB) following high-grain feeding. Six ruminally cannulated goats were divided into two groups: one group was fed a hay diet (COD), and the other group was fed a high grain diet (SAID). Rumen liquids and rumen solids were sampled after 2 weeks adaption. SARA was diagnosed with a pH below 5.8 for 8 h. SAID decreased ruminal pH (P < 0.001) and increased the acetate (P = 0.017), propionate (P = 0.001), butyrate (P < 0.001) and total volatile fatty acid (P < 0.001) concentration in rumen compared with the COD. Denaturing gradient gel electrophoresis fingerprints analysis revealed a clear separation between both the diet and the fraction of rumen digesta in bacterial communities. Pyrosequencing analysis showed that the proportion of phylum Bacteroidetes in the SAID-LAB and SAID-SAB communities was less than in the COD group, whereas the SAID group had a greater percentage of Firmicutes in both the LAB and SAB libraries. UniFrac analyses and a Venn diagram revealed a large difference between the two diets in the diversity of rumen bacterial communities. Overall, our findings revealed that SARA feeding did alter the community structure of rumen liquids and rumen solids. Thus, manipulation of dietary factors, such as ratio of forage to concentrate may have the potential to alter the microbial composition of rumen liquid and rumen solid.
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The objective of this study was to evaluate the changes in bacterial populations in the rumen of dairy cattle following adaptation to subacute ruminal acidosis (SARA) using 16S rRNA gene pyrosequencing. Rumen contents were collected from four cattle adapted to either a 40% (control diet, COD) or 70% (SARA induction diet, SAID) concentrate feeds. DNA was extracted from each of the samples. Bacterial 16S rRNA genes of ruminal DNA extracts were PCR amplified with 2 bar coded primer sets and sequenced by 454 pyrosequencing. At a high taxonomic level, the percentage of Proteobacteria and Bacteroidetes were reduced by SAID feeding, whereas Firmicutes and Actinobacteria were more abundant in the SAID than in the COD group. At the genus level, as compared with the COD group, the abundances of Prevotella, Treponema, Anaeroplasma, Papillibacter, Acinetobacter and unclassified populations including unclassified Lentisphaerae, and unclassified bacteria were lower (P < 0.05), while the percentages of Ruminococcus, Atopobium, unclassified Clostridiales and Bifidobacterium were increased (P < 0.05) in the SAID group. Feeding of SAID reduced (P < 0.001) the diversity of the rumen microbial community. Taken together, our findings provide a comprehensive picture of current knowledge of the community structure of the rumen bacterial ecosystem during SARA, and enhance our understanding about the ruminal microbial ecology that may be useful in the prevention of ruminal acidosis.
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Aim: The aim of this study was to determine the effect of chromium picolinate (CrPic) on the differential expression of the known microRNAs (miRNAs) in broiler skeletal muscle. Methods and results: A total of 288 1-day-old male Arbor Acres broilers were randomly assigned to one of four dietary treatments supplemented with 0, 0.4, 2.0, or 10.0 mg·kg(-1) CrPic, respectively. Dietary CrPic supplementation at 10.0 mg·kg(-1) increased the average daily feed intake in broilers (p < 0.05). On day 42, the serum total protein level was highest in animals treated with 2.0 mg·kg(-1) (p < 0.05) and 10.0 mg·kg(-1) CrPic (p < 0.05). Dietary supplementation with 10.0 mg·kg(-1) CrPic decreased the levels of serum glucose (p < 0.05) on day 42 and of serum triglyceride (p < 0.05) on days 21 and 42. To further identify miRNAs from broiler skeletal muscles, we sequenced two small RNA libraries using the Solexa sequencing approach, and 57 miRNAs were found to be significantly differentially expressed (p < 0.05). Among them, 6 upregulated and 2 downregulated miRNAs were validated by real-time qPCR (p < 0.05). Conclusions: The results of the present study provide a valuable clue regarding the role of miRNA target genes in the mechanism of the dietary CrPic effect on protein synthesis in skeletal muscles of broilers.
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The transition period, from 3 wk before to 3 wk after parturition, is critically important to health, production, and profitability of dairy cows. Most health disorders occur during this time. Compared with other stages of the lactation cycle, relatively little is known about fundamental biological processes during the transition period. The regulation and coordination of lipid metabolism among adipose tissue, liver, gut, and mammary gland are key components of the adaptations to lactation. Lipid accumulation in liver may contribute to health disorders and decreased milk production. Knowledge of key control points in hepatic metabolism of long-chain fatty acids is lacking, as is an understanding of the metabolic effects of hormones, growth factors, and cytokines that mediate stress. Recent evidence indicates that supplemental fats or restricted intakes before parturition can induce a coordinated set of metabolic changes in metabolism of long-chain fatty acids, including peroxisomal β-oxidation, perhaps mediated by peroxisome proliferator-activated receptors. Estimates of the mixture of fuels constituting metabolizable energy in cows during the early postpartum period suggest that supply of amino acids and glucogenic compounds may be under proposed optima, whereas ketogenic and lipogenic compounds and long-chain fatty acids may be in excess. Because dietary fat does not suppress body lipid mobilization, during the early post-partum period supplemental fat may further imbalance the mixture of fuels and lead to decreased dry matter intake. Increased understanding of the biology of the transition period should decrease health problems and increase profitability of dairy cows.
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Summary An in vivo and in vitro fermentation study was conducted in conjunction with a feed intake study to characterize ruminant feed intake and rumen microbial fermentation patterns as steers were adapted to high concen- trate corn and wheat diets. Steers fed the wheat based diet consumed less (P
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Abstract 1. The addition of yeast cell wall (YCW) mannan fractions or low concentrations of antibiotics to the diet of broilers positively affects gut health by improving intestinal cell morphology and improves feed efficiency and performance; however the exact mechanisms are unclear. Based on these production responses, the objective of this study was to compare the effects of supplementing YCW and bacitracin methylene disalicylate (BMD) in the diet on mRNA levels in the jejunum of 6-week-old broilers. 2. Dietary treatments were a maize-soya control diet and the control diet with the addition of YCW or BMD. Birds (n = 7) from each dietary treatment were randomly selected and killed at d 42. Whole jejunum (with serosa) samples were collected for RNA isolation. Gene expression analysis was performed using the AffymetrixGeneChip Chicken Genome Array (Santa Clara, CA, USA). 3. Supplementation with YCW resulted in 928 genes that were significantly changed (456 down-regulated, 472 up-regulated) and supplementation with BMD resulted in 857 genes that significantly changed (408 down-regulated, 449 up-regulated). In addition, 316 genes were significantly changed by both YCW and BMD (146 down-regulated, 170 up-regulated). 4. BMD increased the expression of genes involved in lipid and carbohydrate metabolism and decreased expression of genes associated with T-helper cell pathways. Gene expression profiles from birds fed on diets containing YCW showed changes on a genomic level that correspond to slower gut cell turnover and therefore increased energy preservation for growth. 5. In conclusion, supplementation with BMD or YCW had similar influences on the number of differentially expressed genes in the jejunum. Biological functions common to both YCW and BMD with positive activation scores included antiviral response and antimicrobial response. Genes that were affected by BMD or YCW classified into both different and common biological functions and pathways related to improved metabolism and health in the jejunum.
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Studies in rats and mice have established that maternal nutrition induces epigenetic modifications, sometimes permanently, that alter gene expression in the fetus, which in turn leads to phenotypic changes. However, limited data is available on the influence of maternal diet on epigenetic modifications and gene expression in sheep. Therefore, the objectives of this study were to investigate the impact of different maternal dietary energy sources on the expression of imprinted genes in fetuses in sheep. Ewes were naturally bred to a single sire and from days 67 ± 3 of gestation until necropsy (days 130 ± 1), they were fed one of three diets of alfalfa haylage (HY; fiber), corn (CN; starch), or dried corn distiller's grains (DG; fiber plus protein plus fat). A total of 26 fetuses were removed from the dams and longissimus dorsi, semitendinosus, perirenal adipose depot, and subcutaneous adipose depot tissues were collected for expression and DNA methylation analyses. Expression analysis of nine imprinted genes and three DNA methyltransferase (DNMTs) genes showed significant effects of the different maternal diets on the expression of these genes. The methylation levels of CpG islands of both IGF2R and H19 were higher in HY and DG than CN fetuses in both males and females. This result is consistent with the low amino acid content of the CN diet, a source of methyl group donors, compared to HY and DG diets. Thus, results of this study provide evidence of association between maternal nutrition during pregnancy and transcriptomic and epigenomic alterations of imprinted genes and DNMTs in the fetal tissues.