Transcriptome profiling and functional analysis of sheep fed with high zinc-supplemented diet: A nutrigenomic approach

Genome-wise engineering of ruminant nutrition- nutrigenomics: applications, challenges, and future perspectives – a review

Use of genomic information in ruminant production systems can help relieve concerns related to food security and sustainability of production. Nutritional genomics (i.e., Nutrigenomics) is a field of research that is interested in all types of reciprocal interactions between nutrients and genomes of organisms, i.e., variable patterns of gene expression and effect of genetic variations on the nutritional environment. Devising a revolutionizing analytical approach to traditional ruminant nutrition research, the relatively novel area of ruminant nutrigenomics has several studies concerning different aspects of animal production systems. This paper aims to review the current nutrigenomics research in the frame of how nutrition of ruminants can be modified accounting for individual genetic backgrounds and gene/diet relationships behind productivity, quality, efficiency, disease resistance, fertility, and GHG emissions. Furthermore, current challenges facing ruminant nutrigenomics are evaluated and future directions for the novel area are strongly argued by this review.

Proteolytic Volatile Profile and Electrophoretic Analysis of Casein Composition in Milk and Cheese Derived from Mironutrient-Fed Cows

The aim of the study was to evaluate the proteolytic process in Caciocavallo cheese obtained from Friesian cows fed zinc, selenium, and iodine supplementation. Thirty-six Friesian cows, balanced for parity, milk production, and days in milk, were randomly assigned to four groups. The control group (CG) was fed with a conventional feeding strategy, while the three remaining groups received a diet enriched with three different trace elements, respectively zinc (ZG), selenium (SG), and iodine (IG). At the end of the experimental period, samples of milk were collected and used to produce Caciocavallo cheese from each experimental group. Cheese samples were then analyzed after 7 and 120 days from the cheese making in order to obtain information on chemical composition and extent of the proteolytic process, evaluated through the electrophoretic analysis of caseins and the determination of volatiles profile. Both milk and cheese samples were richer in the amount of the microelement respectively used for the integration of the cattle’s diet. The zymographic approach was helpful in evaluating, in milk, the proteolytic function performed by endogenous metalloenzymes specifically able to degrade gelatin and casein; this evaluation did not highlight significant differences among the analyzed samples. In cheese, the electrophoretic analysis in reducing and denaturing condition showed the marked ability of β-casein to resist the proteolytic action during ripening, whereas the dietary selenium supplementation was shown to perform a protective action against the degradation of S1 and S2 isoforms of α-casein. The analysis of the volatile profile evidenced the presence of compounds associated with proteolysis of phenylalanine and leucine. This approach showed that selenium was able to negatively influence the biochemical processes that lead to the formation of 3-methyl butanol, although the identification of the specific mechanism needs further investigation.

Influence of Zinc Feeding on Nutritional Quality, Oxidative Stability and Volatile Profile of Fresh and Ripened Ewes' Milk Cheese

Zinc represents a ubiquitous element in cells with relevant roles in the metabolism of essential nutrients in animals. The aim of this study was to investigate the effect of dietary zinc supplementation on nutritional and aromatic properties of milk and Pecorino cheeses obtained from lactating ewes. Fifty-two commercial ewes were randomly assigned to two groups. The control group was fed with a conventional complete diet, while the experimental group received a daily supplementation of 375 mg/head of zinc oxide. At the end of the trial, which lasted 30 days, samples of milk and related cheese were collected in order to obtain information about the chemical composition and volatile profile. The experimental feeding strategy induced a significant increase in zinc concentration in milk. Furthermore, both in milk and cheese, was observed an increase in vaccenic, rumenic and total polyunsaturated fatty acids, with the consequent significant reduction of atherogenic and thrombogenic indices. The volatile profile of dairy products was also positively affected by dietary zinc intake, with an increase in concentration of hexanoic acid and ethyl esters. The present study suggests interesting possible effects of dietary zinc supplementation of ewes in improving the nutritional characteristics of fresh and ripened dairy products, although more specific and in-depth assessments should be performed on these new products, in order to characterize potential variations on consumers acceptability.

Whole blood transcriptome analysis in ewes fed with hemp seed supplemented diet

The hemp plant (Cannabis sativa L.) has a long tradition of being used for many different purposes such as industry, medicine and nutrition. In particular, because hemp seed (HS) is rich in oil protein and considerable amounts of dietary fiber, vitamins and minerals that are particularly suitable also for animal nutrition. Different studies have evaluated HS on qualitative and quantitative properties of livestock products but as of today, nobody has investigated the molecular pathway behind HS supplementation in farm animals. Thus, in this study, we will report the first RNA sequencing of the whole-blood transcriptome of ewes fed either with a controlled diet (CTR, n = 5) or with a diet supplemented with 5% of hemp seed (HSG, n = 5). Applying a false discovery rate (FDR) <0.05 and a log₂FC either higher than 0.5 or lower than −0.5, we identified 314 differentially regulated genes in the HS-supplemented group compared to the CTR group. Several genes encoding for different subunits belonging to the complex I, II, III, IV and ATP-synthase were up-regulated making oxidative phosphorylation (FDR: 3.05e-19) and thermogenesis (FDR: 2.17e-16) the highest up-regulated pathways in our study. Moreover, we found up-regulation in different genes involved in lactose biosyntheses such as GALK1 and PGM1 and, as a result, we observed a statistically higher lactose percentage in the HSG group (p < 0.05). These results indicate that HS supplementation positively affects the energy production pathway in lactating ewes conferring them also more resistance to adverse climatic conditions such as low temperature. Finally, the higher milk lactose content makes the derived dairy products more profitable.

Whole blood transcriptome analysis in ewes fed with hemp seed supplemented diet

The hemp plant (Cannabis sativa L.) has a long tradition of being used for many different purposes such as industry, medicine and nutrition. In particular, because hemp seed (HS) is rich in oil protein and considerable amounts of dietary fiber, vitamins and minerals that are particularly suitable also for animal nutrition. Different studies have evaluated HS on qualitative and quantitative properties of livestock products but as of today, nobody has investigated the molecular pathway behind HS supplementation in farm animals. Thus, in this study, we will report the first RNA sequencing of the whole-blood transcriptome of ewes fed either with a controlled diet (CTR, n = 5) or with a diet supplemented with 5% of hemp seed (HSG, n = 5). Applying a false discovery rate (FDR) <0.05 and a log₂FC either higher than 0.5 or lower than -0.5, we identified 314 differentially regulated genes in the HS-supplemented group compared to the CTR group. Several genes encoding for different subunits belonging to the complex I, II, III, IV and ATP-synthase were up-regulated making oxidative phosphorylation (FDR: 3.05e-19) and thermogenesis (FDR: 2.17e-16) the highest up-regulated pathways in our study. Moreover, we found up-regulation in different genes involved in lactose biosyntheses such as GALK1 and PGM1 and, as a result, we observed a statistically higher lactose percentage in the HSG group (p < 0.05). These results indicate that HS supplementation positively affects the energy production pathway in lactating ewes conferring them also more resistance to adverse climatic conditions such as low temperature. Finally, the higher milk lactose content makes the derived dairy products more profitable.

Iodine Supplemented Diet Positively Affect Immune Response and Dairy Product Quality in Fresian Cow

The effects of iodine supplementation on the whole-transcriptome of dairy cow using RNA sequencing has been investigated in this study. Iodine did not influence the milk composition, while an improvement was observed in the immune response as well as in the quality of dairy product. Indeed, the iodine intake specifically influenced the expression of 525 genes and the pathway analysis demonstrated that the most affected among them were related to immune response and oxidative stress. As a consequence, we indirectly showed a better response to bacterial infection because of the reduction of somatic cell counts; furthermore, an improvement of dairy product quality was observed since lipid oxidation reduced in fresh cheese. Such findings, together with the higher milk iodine content, clearly demonstrated that iodine supplementation in dairy cow could represent a beneficial practice to preserve animal health and to improve the nutraceutical properties of milk and its derived products.

Whole-transcriptome profiling of sheep fed with a high iodine-supplemented diet

Iodine (I) is a micronutrient that mammals need for proper functionality of thyroid gland since it is the main component of thyroid hormones. Besides studies that have investigated the role of I in livestock nutrition, it is also important to know the transcriptomics changes in small ruminants following I supplementation. Therefore, the aim of this study was to investigate the effects of I on the whole blood transcriptome in sheep. Fifteen lactating cross-bred ewes (3 to 4-year-old, 55 to 65 kg BW) at their late lactation period were enrolled in this study. At the beginning, all the animals had a 2-week acclimation period where they were fed with a basal diet which includes an adequate level of I (2 mg I/animal per day) in the form of calcium iodate (CaI2O6). Then, the ewes were randomly divided into two groups and fed in individual troughs: the control group (n = 5) was maintained on basal diet and the experimental group (I, n = 10) was fed for 40 days with a diet containing a high I supplementation (equivalent to 30 mg I/animal per day), in the form of potassium iodide. Whole blood and milk were collected individually at the beginning (T0) and after the 40 days of supplementation (T40). Iodine quantification was assessed in serum and milk sample. Microarray gene expression analysis was performed on whole blood and, filtering data using a fold change >2 with an adjusted P < 0.05, we identified 250 differentially expressed genes (DEGs) in the I group (T40 v. T0). Looking for biological processes associated with our DEGs, we found significant association with cell growth regulation. Thus, our study unveils the role of I supplementation on gene expression in sheep improving the knowledge about micronutrients in animal nutrition.

Whole Blood Transcriptome Analysis Reveals Positive Effects of Dried Olive Pomace-Supplemented Diet on Inflammation and Cholesterol in Laying Hens

Simple Summary

Olive pomace (OP) represents an important source of bioactive compounds which have been successfully used for animal nutrition. In this study, we elucidate the whole transcriptome of laying hens fed with a dried OP (DOP)-supplemented diet using an RNA sequencing approach. We found that DOP modulates several biological pathways mainly related to inflammatory response and cholesterol biosynthesis. Consistent with the gene expression data, we noted a decrease of egg yolk cholesterol. Thus, our study provides evidence that a DOP-supplemented diet improves egg quality and, at the same time, ameliorates inflammatory animal status.

Abstract

Olive pomace (OP) represents one of the by-products of the olive industry and represents an important source of bioactive compounds. This characteristic makes OP a potential feed supplement in livestock nutrition. Thus, in the last years, several studies have been published to evaluate the productive traits following OP supplementation in animal diets; however, relatively little is known from a molecular biology standpoint. Therefore, in this study, we report the RNA-sequencing analysis of laying hens fed with a 10% dried OP (DOP) supplementation. Applying a false discovery rate (FDR) <0.05 and a Log₂Fc either less than −1.5 or higher than +1.5, we identified 264 differentially regulated genes (DEGs) between the non-supplemented diet control group (CTR) and the DOP group. Using the 264 DEGs to identify enriched biological pathways, we noted that cholesterol biosynthesis showed the highest enrichment followed by several pathways related to immune response and inflammation. As a consequence, when we quantified the cholesterol amount in yolk egg, we found a significant reduction in the DOP vs. the CTR group (p < 0.05). In conclusion, this study shows that DPO affects gene expression in laying hens, which is directly correlated with cholesterol decrease and can potentially ameliorate health status influencing immune response and inflammation.

RNA Sequencing-Based Whole-Transcriptome Analysis of Friesian Cattle Fed with Grape Pomace-Supplemented Diet

Simple Summary

Grape pomace (GPO) is an important source of polyphenols which are known to have antioxidant properties. In the past decade, GPO has received some attention as a bioactive dietary component in farm animals’ diet. In this study, we have analyzed the whole-transcriptome of Friesian calves fed with a GPO-supplemented diet using RNA-sequencing. We noted that the most affected pathway was the cholesterol lipid biosynthesis and this effect was consistent with a reduction in both serum cholesterol and lipid oxidation in the carcasses. This study provides evidence on the antioxidant property of GPO-supplemented diet, from a molecular biology standpoint.

Abstract

Grape pomace (GPO), the main by-product of the wine making process, is a rich source of polyphenols with potent antioxidant properties. Recently, GPO has emerged as a potential feed additive in livestock nutrition, with several reports describing its beneficial effects on animals’ overall health status or production traits. However, little is known about it from a molecular biology standpoint. In the present study, we report the first RNA sequencing-based whole-transcriptome profiling of Friesian calves fed with a GPO-supplemented diet. We identified 367 differentially expressed genes (p < 0.05) in the GPO-supplemented calves (n = 5), when compared with unsupplemented control group (n = 5). The pathway analysis showed that ‘cholesterol lipid biosynthesis’ was the most negatively-enriched (p < 0.001) pathway in the GPO-supplemented animals. In specific terms, five important genes coding for cholesterol biosynthesis enzymes, namely the Farnesyl-diphosphate Farnesyltransferase 1 (FDFT-1), Squalene Epoxidase (SQLE), NAD(P)-dependent Steroid Dehydrogenase-like (NSDHL), Methylsterol Monooxygenase (MSMO)-1, and Sterol-C5-desaturase (SC5D), two major transcription factors (the Sterol Regulatory Element-binding Transcription Factor 1 and 2), as well as the Low-Density Lipoprotein Receptor (LDLR), were all downregulated following GPO supplementation. Such an effect was mirrored by a reduction of blood cholesterol levels (p = 0.07) and a lowered (p < 0.001) Malondialdehyde (lipid oxidation marker) level in carcasses. We provide evidence on the effects of GPO-supplemented diets on the whole-transcriptome signature in veal calves, which mainly reflects an antioxidant activity.