The discovery of new protein-coding DNA variants related to carcass traits is very important for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer the opportunity to focus on the regions of DNA potentially related to the gene and protein expression. In this research a human commercial target enrichment kit was used to evaluate its performances for pig exome capture and for the identification of DNA variants suitable for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa (ENSEMBL Sus_scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and 35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a total of 232,530 single nucleotide variants (SNVs) of which 20.6% mapped in exonic regions and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom MassARRAY® system confirms that this "human-on-pig" approach offers new potentiality for the identification of DNA variants in protein-coding genes.

Dietary partially destoned olive cake supplementation on performance, carcass traits and meat quality of intensively finished bulls was evaluated. Forty-five Limousin bulls, divided into three homogenous groups, received a diet with no supplementation (Control-CTR), 7.5% (Low Olive Cake-LOC), and 15.0% of olive cake supplementation (High Olive Cake-HOC). The trial was realized for 150 days; all bulls were individually weighed at the beginning, middle, and end of the trial, to calculate the individual average daily gain (ADG). At slaughtering, on each carcass, hot weight was recorded and, after 7 days, the pH and temperature were measured. On Longissimus lumborum muscle, color, cooking loss, and shear force of the cooked sample were determined. The chemical composition and the fatty acid content of muscle were determined. Olive cake inclusions (7.5% and 15.0%) increased (p < 0.05) the body weight, ADG, slaughter traits and intramuscular fat content and influenced (p < 0.05) the quality indices. The 15.0% of the inclusion reduced (p < 0.05) the cooking loss and shear force, and increased the unsaturated fatty acid content. The olive cake can be considered as a functional component in beef production and, in substitution to a quote of cereals into the diet of bulls, could be an opportunity to improve agriculture sustainability.

Aim of the present study was to assess the effect of dietary dried partially destoned olive cake supplement on nutritional quality and sensory profile of milk and cheese produced by dairy cows. The experiment was carried out on eighty-four healthy dairy Friesian cows divided into two homogenous groups. The control group (CTR) received a conventional diet, whereas the experimental group (OC) received a conventional diet supplemented with olive cake as 15% of DM. The trial lasted five months. Monthly, on individual milk samples, yield and physical-chemical parameters were determined. Milk was used for the artisanal cheese production. On 10 samples of cheese for each group, physical-chemical and fatty acid profile were determined. Electronic nose analysis and sensory evaluation were performed. Data were analyzed by ANOVA. The diet affected (p < 0.05) the milk yield, exclusively in September. Yield and quality of cheese of OC group after 60 d of ripening showed higher (p < 0.05) yield, moisture and fat content, lower (p < 0.05) pH, protein, salt and ash content, higher (p < 0.01) MUFA and PUFA and CLA content, lower (p < 0.05) SFA, higher (p < 0.01) UFA/SFA and hypocholesterolemic/hypercholesterolemic ratios, better (p < 0.01) atherogenic and thrombogenic indices. Data show dietary olive cake supplementation in lactating dairy cows improves nutritional and nutraceutical properties of cheese, volatile profile and level of assessors' acceptance.

Oxidative stress causes several pathological conditions in humans and animals, including gastrointestinal disorders. The aim of this study was to analyze the antioxidant capacity of three natural powdered raw materials containing quercetin, bromelain, and Lentinula edodes and develop a new feed supplement for dogs using a combination of them. The total phenolic content (TPC), antioxidant activity, DPPH (2,2-diphenyl-1-picrylhydrazyl), and ABTS (2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt) of the extracts, either individually or in combination, were evaluated colorimetrically. The effects of this supplement on healthy adult dogs' nutritional, inflammatory, and stress status were evaluated. American Staffordshire Terrier adult female dogs (n = 30) were randomly assigned to a control (n = 15) or a treated (n = 15) group. The supplement was added as powder to the food of the treated dogs once daily for 28 days. There was no significant difference in the body weight and body condition scores between the initial and final phases of the experiment. At the end of our study, a significant decrease in fecal calprotectin, cortisol, indole/skatole, and N-methylhistamine and a significant increase in short-chain fatty acids were observed as compared to the control group. In conclusion, this natural feed supplement can be used to improve gastrointestinal health and psycho-physical conditions in dogs.

Recent studies have found bacterial DNA in the blood of healthy individuals. To date, most studies on the blood microbiome have focused on human health, but this topic is an expanding research area in animal health as well. This study aims to characterize the blood microbiome of both healthy dogs and those with chronic gastro-enteropathies. For this study, blood and fecal samples were collected from 18 healthy and 19 sick subjects, DNA was extracted through commercial kits, and the V3-V4 regions of the 16S rRNA gene were sequenced on the Illumina platform. The sequences were analyzed for taxonomic annotation and statistical analysis. Alpha and beta diversities of fecal microbiome were significantly different between the two groups of dogs. Principal coordinates analysis revealed that healthy and sick subjects were significantly clustered for both blood and fecal microbiome samples. Moreover, bacterial translocation from the gut to the bloodstream has been suggested because of found shared taxa. Further studies are needed to determine the origin of the blood microbiome and the bacteria viability. The characterization of a blood core microbiome in healthy dogs has potential for use as a diagnostic tool to monitor for the development of gastro-intestinal disease.

This study examined microRNA (miRNAs) expression and regulatory patterns from milk exosomes of cows experienced group relocation, a common husbandry practice during the lactation period and used as a spontaneous model of stress. Total RNA from milk exosome samples was collected from 3 cows that showed an increased milk cortisol (HRC) after relocation (T2 vs T1) and 3 cows that did not show cortisol increase (LRC). A total of 69 known miRNAs were identified. Thirteen miRNAs were consistently down-regulated at T2 in comparison to T1, such as miR-2904-1, miR-142, miR-2284x and miR-30b-3p. Only two miRNAs, miR-2284z and miR-146a were significantly different between LRC and HRC group. Functional enrichment analyses highlighted that glucocorticoid receptor signaling and neurotrophic factor mediated TRK receptor signaling were among the biological pathways affected by differentially expressed miRNA target genes. Mir-135a-5p and miR-320a were involved in both biological pathways. miR-142-5p, miR-142-3p, miR-30b-5p and miR-320a shared the same target genes belonging to the RAS superfamily of small GTP-binding proteins (RAC1, RAP1A and RASA1), involved in neurotrophin-mediated cell survival. MiR-142, miR-135 and miR-320a in milk exosomes were the most responsive to group relocation of cows.

Dairy cattle health, wellbeing and productivity are deeply affected by stress. Its influence on metabolism and immune response is well known, but the underlying epigenetic mechanisms require further investigation. In this study, we compared DNA methylation and gene expression signatures between two dairy cattle populations falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine marker of stress in dairy cows. Reduced Representation Bisulfite Sequencing was used to obtain a methylation map from blood samples of these animals. The high and low groups exhibited similar amounts of methylated CpGs, while we found differences among non-CpG sites. Significant methylation changes were detected in 248 genes. We also identified significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) analysis showed that genes of both groups act together in several pathways, such as nervous system activity, immune regulatory functions and glucocorticoid metabolism. These preliminary results suggest that, in livestock, cortisol secretion could act as a trigger for epigenetic regulation and that peripheral changes in methylation can provide an insight into central nervous system functions.

Protected Designation of Origin (PDO) dry-cured ham is the most important product in the Italian pig breeding industry, mainly oriented to produce heavy pig carcasses to obtain hams of the right weight and maturity. Recently, along with the traditional traits swine breeding programs have aimed to include novel carcass traits. The identification at the genome level of quantitative trait loci (QTLs) affecting such new traits helps to reveal their genetic determinism and may provide information to be integrated in prediction models in order to improve prediction accuracy as well as to identify candidate genes underlying such traits. This study aimed to estimate genetic parameters and perform a single step genome wide association studies (ssGWAS) on novel carcass traits such as untrimmed (UTW) and trimmed thigh weight (TTW) in two pig crossbred lines approved for the ham production of the Italian PDO. With this purpose, phenotypes were collected from ~1800 animals and 240 pigs were genotyped with Illumina PorcineSNP60 Beadchip. The single-step genomic BLUP procedure was used for the heritability estimation and to implement the ssGWAS. QTL were characterized based on the variance of 10-SNP sliding window genomic estimated breeding values. Moderate heritabilities were detected and QTL signals were identified on chromosome 1, 4, 6, 7, 11 and 15 for both traits. As expected, the genetic correlation among the two traits was very high (~0.99). The QTL regions encompassed a total of 249 unique candidate genes, some of which were already reported in association with growth, carcass or ham weight traits in pigs. Although independent studies are required to further verify our findings and disentangle the possible effects of specific linkage disequilibrium in our population, our results support the potential use of such new QTL information in future breeding programs to improve the reliability of genomic prediction.

The aim of the study was to assess the inclusion of different levels of olive cake in pigs' diet as a strategy to replace conventional ingredients and to improve meat quality traits. Seventy-two Pietrain pigs, during the growing-finishing period (50-120 kg BW), were fed with three dietary treatments that contained or did not contain olive cake: 0% (Ctrl), 5% (Low), and 10% (High). The trial lasted 90 days. Weekly, individual body weight (BW) and feed intake (FI) were recorded to calculate average daily gain (ADG) and feed conversion ratio (FCR). At slaughter, the dressing percentage was calculated and carcass weight and backfat thickness were measured. On a section of Longissimus thoracis muscle (LT), pH, color, chemical, and fatty acid composition were determined. Fatty acid profile was also determined in backfat. The statistical model included the effects of diet (Ctrl, Low, and High). The inclusion of 5% of olive cake in the diet improved significantly (p < 0.05) BW and FCR. Both levels of inclusion (5% and 10%) significantly reduced (p < 0.05) backfat thickness and intramuscular fat and modified their fatty acid composition, increasing (p < 0.05) the concentration of MUFA and PUFA and improving (p < 0.05) quality indices. Results suggest that olive cake did not negatively affect the productive performances.

The study was conducted to investigate the effects of dietary administrations of four nutraceuticals in dogs. Seventy four dogs were enrolled in the trials, 24 healthy dogs were fed with a control diet (CT) and the experimental groups received for 60days the same diet supplemented with nutraceuticals, namely Echinacea angustifolia (EA, 0.10mg/kg live weight as echinacoside; 14 dogs), Vaccinium myrtillus (VM, 0.20mg/kg live weight as anthocyanidin, 13 dogs), Curcuma longa (CL, 6.60mg/kg live weight as curcumin, 18 dogs with arthrosis), and Sylibum marianum (SM, 1.5mg/kg live weight as sylibin, 8 dogs with hepatopathy). Dogs were weighted at the beginning of study and blood samples were collected at the beginning (T0) and at the end (T60) of the study. VM significantly down regulated TNF, CXCL8, NFKB1 and PTGS2 and decreased plasma ceruloplasmin (CuCp). The activity of EA was evidenced by the significant decrease of TNF and NFKB1 expression and CuCp levels and by the increase of plasma Zn. Administration of CL caused a significant decrease of CuCp and increase of Zn and a down regulation of TNF, CXCL8, NFKB1 and PTGS2, corroborating the anti-inflammatory action of curcuminoids. After 60days of treatment with SM, plasma ALT/GPT activity was reduced and paraoxonase was increased, supporting the antioxidant activity of silymarin, also confirmed by the significant up regulation of SOD2. Results indicated that nutraceutical administrations in dogs can be an interesting approach to modulate immune response in order to improve health condition of animals.

The purpose of the study is to determine the nutritional characteristics of some by-products derived from fruit juice and olive oil production to evaluate their use in pig nutrition. Five by-products of citrus fruit (three citrus fruit pulp and two molasses) and three by-products of olive oil (olive cake) obtained by different varieties are analysed for chemical composition. The fermentation characteristics are evaluated in vitro using the gas production technique with swine faecal inoculum. All the citrus by-products are highly fermentable, producing gas and a high amount of short-chain fatty acids. The fermentation kinetics vary when comparing pulps and molasses. Citrus fruit pulps show lower and slower fermentation rates than molasses. The olive oil by-products, compared to citrus fruits ones, are richer in NDF and ADL. These characteristics negatively affect all the fermentation parameters. Therefore, the high concentration of fiber and lipids represents a key aspect in the nutrition of fattening pigs. The preliminary results obtained in this study confirm that the use of by-products in pig nutrition could represent a valid opportunity the reduce the livestock economic cost and environmental impact.

With the aim to explore the use of A. hypochondriacus seeds for animal feeding, the agronomic traits, nutrients, and bioactive compounds of four accessions with different origin (India, Nebraska, Iowa, and Pennsylvania) grown in a Mediterranean environment were studied. Proximate composition was determined using the official methods of analyses, fatty acid profile by gas chromatography, total phenolic content (TPC) and the scavenging activity (DPPH• and ABTS•+) by colorimetric method. A one-way ANOVA model was performed to determine the differences between accessions. The four A. hypochondriacus accessions showed interesting seed yield results. No significant differences were observed for crude protein and crude fiber; the oil content showed the significant highest values in the seeds from Nebraska and Pennsylvania, but their nutritional characteristics were significantly different. The accession from Nebraska showed the highest oleic and linoleic acid levels, the highest values of polyunsaturated fatty acids, the best atherogenic and thrombogenic indices and hypocholesterolemic/hypercholesterolaemic ratio, and the highest TPC content. The accession from Pennsylvania showed the highest antioxidant activity and lowest peroxidation index. On the whole, A. hypochondriacus seeds can be used as pseudo-cereal to balance the animal diet and the accession should be chosen according to the different metabolic pathways of unsaturated fatty acids in ruminant and monogastric animals.

Several studies have underlined the interplay among host-microbiome and pathophysiological conditions of animals. Research has also focused specifically on whether and how changes in the gut microbiome have provoked the occurrence of pathological phenomena affecting cartilage and joints in humans and in laboratory animals. Here, we tried to evaluate the relationship between the gut microbiome and the hip and elbow arthritis in owned dogs. The study included 14 dogs suffering from chronic arthritis (AD) and 13 healthy dogs (HD). After the first visit and during the period of the study, the dogs, under the supervision of the owner, were fed a semi-moist complete diet supplemented with omega 3 fatty acids. Feces and blood samples were collected in the clinic at the first visit (T0) and after days (T45). The plasma C-reactive protein (CRP) was higher, and the serum vitamin B12 and folate concentrations were lower (p < 0.05) in the AD group in comparison to the HD group. Data of the fecal microbiome showed that the relative abundances of the genus Megamonas were higher in AD (p < 0.001), while the relative abundance of the families Paraprevotellaceae, Porphyromonadaceae, and Mogibacteriaceae was significantly lower in comparison to HD. The results of the study identified several bacterial groups that differed significantly in the fecal microbiome between healthy and diseased dogs. If the observed differences in fecal bacterial composition predispose dogs to hip and elbow arthritis or if these differences reflect a correlation with these conditions deserves further investigation.

Stress in livestock reduces productivity and is a welfare concern. At a physiological level, stress is associated with the activation of inflammatory responses and increased levels of harmful reactive oxygen species. Biomarkers that are indicative of stress could facilitate the identification of more stress-resilient animals. We examined twenty-one metabolic, immune response, and liver function biomarkers that have been associated with stress in 416 Italian Simmental and 436 Italian Holstein cows which were genotyped for 150K SNPs. Single-SNP and haplotype-based genome-wide association studies were carried out to assess whether the variation in the levels in these biomarkers is under genetic control and to identify the genomic loci involved. Significant associations were found for the plasma levels of ceruloplasmin (Bos taurus chromosome 1-BTA1), paraoxonase (BTA4) and γ-glutamyl transferase (BTA17) in the individual breed analysis that coincided with the position of the genes coding for these proteins, suggesting that their expression is under cis-regulation. A meta-analysis of both breeds identified additional significant associations with paraoxonase on BTA 16 and 26. Finding genetic associations with variations in the levels of these biomarkers suggests that the selection for high or low levels of expression could be achieved rapidly. Whether the level of expression of the biomarkers correlates with the response to stressful situations has yet to be determined.

The characterization of the microbial population in different compartments of the organism, such as the gastrointestinal tract, is now possible thanks to the use of high-throughput DNA sequencing technique. Several studies in the companion animals field have already investigated the fecal microbiome in healthy or sick subjects; however, the methodologies used in the different laboratories and the limited number of animals recruited in each experiment do not allow a straight comparison among published results. Previously, our research focused on the characterization of the microbial taxa variability in 340 fecal samples from 132 healthy dogs, collected serially from several in-house experiments. The results supported the responsiveness of microbiota to dietary and sex factors and allowed us to cluster dogs with high accuracy. For the present study, intestinal and blood microbiota of healthy dogs from different breeds, genders, ages and food habits were collected, with three principal aims: firstly, to confirm the results of our previous study regarding the fecal microbiome affected by the different type of diet; secondly, to investigate the existence of a blood microbial population, even in heathy subjects; and thirdly, to seek for a possible connection between the fecal and the blood microbiota. Limited researches have been published on blood microbiota in humans, and this is the first evidence of the presence of a bacterial population in the blood of dogs. Moreover, gut and blood microbiota can discriminate the animals by factors such as diet, suggesting some relationship between them. These preliminary results make us believe in the use of the blood microbiome for diagnostic purposes, such as researching and preventing gut inflammatory diseases.

The aim of this study was to evaluate the effect of the administration of Saccharomyces boulardii on the nutritional, immunological, inflammatory, and stress status and on the composition of the gut microbiota and mycobiota in healthy adult dogs. A total of 25 American Staffordshire Terrier dogs were selected and randomly assigned to two groups: control (CTR, n = 12) and treated (TRT, n = 13) groups. No significant differences were found between the two groups regarding body weight, body condition score, and fecal score. No significant differences in microbiota/mycobiota, short chain fatty acids, indole/skatole, histamine, zonulin, or lactoferrin were detected. Indeed, supplementation with S. boulardii significantly decreased fecal calprotectin Immunoglobulin A, indicating an improvement in the gut well-being. Interestingly, fecal cortisol significantly decreased in dogs belonging to the TRT group compared to the CTR, suggesting both an improvement of the intestinal status and a reduction of stress, a common condition affecting animals managed in a breeding environment.

Arctium lappa (AL), Camellia sinensis (CS), Echinacea angustifolia, Eleutherococcus senticosus, Panax ginseng (PG), and Vaccinium myrtillus (VM) are plants traditionally used in many herbal formulations for the treatment of various conditions. Although they are well known and already studied for their anti-inflammatory properties, their effects on H2O2-stimulated macrophages are a novel area of study.

Agronomic traits, oil content, fatty acid composition, antioxidant activity, and total phenolic content were studied on eight A. cruentus accessions cultivated in Southern Italy. A one-way ANOVA model was performed to compare accessions and the Principal Components Analysis was applied to identify patterns in our dataset and highlight similarities and differences. A. cruentus showed valuable seed yield (0.27 kg/m2, on average) comparable to the main tradition cereals used for animal feeding. Seed-oil composition showed significant differences among the accessions. Data showed a higher lipid content than most cereal grains (from 5.6 to 7.3%). Approximately 60% of fatty acids were unsaturated; linoleic fatty acid ranged from 19 to 34%, oleic acid from 29 to 36%, and alfa-linolenic fatty acid from 0.3 to 0.5%, respectively. The saturated/unsaturated fatty acid ratio ranged from 0.5 to 0.8, the hypocholesterolemic:hypercholesterolaemic ratio from 1.7 to 2.7, the Atherogenic Index from 0.38 to 0.66, the Thrombogenic Index from 0.85 to 1.48, the total phenolic content from 0.14 to 0.36 mg/g seeds, and the antioxidant activity (DPPH•) from 0.30 to 0.50. The studied seed-oil composition evidenced A. cruentus as a healthy ingredient for animal feed and consequently, as a possible substitute for traditional cereals. Accessions from Mexico and Arizona emerged for their high qualitative traits.

The characterization of the microbial population of many niches of the organism, as the gastrointestinal tract, is now possible thanks to the use of high-throughput DNA sequencing technique. Several studies in the companion animals field already investigated faecal microbiome in healthy or affected subjects, although the methodologies used in the different laboratories and the limited number of animals recruited in each experiment does not allow a straight comparison among published results. In the present study, we report data collected from several in house researches carried out in healthy dogs, with the aim to seek for a variability of microbial taxa in the faeces, caused by factors such as diet and sex. The database contains 340 samples from 132 dogs, collected serially during dietary intervention studies. The procedure of samples collection, storage, DNA extraction and sequencing, bioinformatic and statistical analysis followed a standardized pipeline. Microbial profiles of faecal samples have been analyzed applying dimensional reduction discriminant analysis followed by random forest analysis to the relative abundances of genera in the feces as variables. The results supported the responsiveness of microbiota at a genera taxonomic level to dietary factor and allowed to cluster dogs according this factor with high accuracy. Also sex factor clustered dogs, with castrated males and spayed females forming a separated group in comparison to intact dogs, strengthening the hypothesis of a bidirectional interaction between microbiota and endocrine status of the host. The findings of the present analysis are promising for a better comprehension of the mechanisms that regulate the connection of the microorganisms living the gastrointestinal tract with the diet and the host. This preliminary study deserves further investigation for the identification of the factors affecting faecal microbiome in dogs.

Protected Designation of Origin (PDO) dry-cured hams production is greatly dependent on raw meat quality. This study was performed to identify genetic markers associated with the quality of dry-cured ham. Carcass traits of 229 heavy pigs belonging to three commercial genetic lines were registered (weight, EUROP classification). Phenotypic traits (Semimembranosus muscle ultimate pH, ham weight and lean meat content, adsorbed salt) of the corresponding thighs, undergone PDO ham process in three different plants, were measured, using a fast and non-invasive technology. Green ham weight and lean meat percentage influenced the estimated salt content and the weight loss during salting, even if the processing plant greatly affected the variability of the measured ham traits. The genomic data were obtained with the GeneSeek Genomic Profiler (GGP) 70k HD Porcine Array, using the slaughter day and the sex of the animals in the statistical analyses. The phenotypic traits were associated with the genotypes through GenAbel software. The results showed that 18 SNPs located on nine porcine chromosomes were found to be associated with nine phenotypic traits, mainly related to ham weight loss during salting. New associations were found between markers in the genes Neural Precursor Cell Expressed Developmentally Down-Regulated 9 (NEDD9, SSC7), T-Cell Lymphoma Invasion and Metastasis 2 (TIAM2, SSC1), and the ham quality traits. After validation, these SNPs may be useful to improve the quality of thighs for the production of PDO dry-cured hams.