Identification of biological factors that can be consistently linked to performance variation in modern commercial broiler flocks

The intensification of the chicken meat industry over the past 50 years has resulted in a 400% increase in the growth rate of meat birds and a 50% reduction in feed conversion ratio, maintaining poultry as a cost-effective source of protein. Improvements have been a direct result of genetic selection for growth and feed efficiency (85-90%), advances in poultry nutrition and improved management practices. Despite production gains, performance variation remains both within and between broilers strains, which is a negative economic trait resulting in losses to producers and the industry alike. We therefore aimed to elucidate biological factors contributing to variations in growth and performance, particularly in meat birds. As growth has been repeatedly shown to be an immunological trade-off, the first study investigated whether functional changes in intestinal barrier function and innate immunity could be consistently linked to the phenotypic expression of feed conversion ratio (FCR) in meat birds. Genes in the small intestine were investigated between high- and low-performing phenotypes (selected on individual FCR), collected from three separate trials. There was no evidence linking flock performance variation with basal parameters of innate intestinal immunity in the ileum in this study. Higher variation in the expression levels of two genes, Toll-like Receptor 2 (TLR2) and membrane protein CD36 were of interest however, as both exhibit numerous overlapping and individual functions contributing to both innate immunity and fatty acid metabolism. A second study was conducted to investigate whether links between innate immunity and fatty acid metabolism could be contributing to variations in growth and performance. Total carcass fat %, carcass and blood lipid composition, key genes involved in fatty acid metabolism and selected innate immune parameters were investigated in meat birds, layer birds and F1 layer x meat bird crosses at d14 post hatch. The results indicated a total upregulation of fatty acid metabolism in meat birds when compared to the F1 cross and layer birds, for both fatty synthesis as well as β-oxidation in the liver, suggestive of altered metabolism. There was no evidence to suggest that any birds were exhibiting cellular hepatic stress or that fatty acid metabolism was interacting with parameters of innate immunity in this study. A third study used RNA-Seq to compare liver transcriptomes of meat birds, layer birds and their F1 cross. The objective was to identify differentially expressed (DE) genes between differing growth phenotypes to identify genes and biological pathways contributing to growth variations. Of the total genes identified, 155 were DE between all three groups. Transcriptional differences between the groups were large, particularly between meat birds and layers. Of the genes analysed, 19% were DE between meat birds and layers; 9.6% of genes DE between meat birds and cross; and 1.6% of genes DE between cross and layer birds. The most significant finding was the repeated enrichment of the FoxO signalling pathway, particularly genes related to cell cycle regulation and the insulin receptor. There was also a high correlation between FoxO pathway genes and bodyweight, as well as genes related glycolysis and bodyweight. In summary, this thesis explores several biological factors associated with growth and performance variation in commercial meat birds. The results indicated that intestinal barrier/innate immune function was not associated with the phenotypic expression of FCR nor was altered immune function detected with differential fatty acid metabolism between birds differing in growth potential. There was however significant evidence implicating the FoxO signalling pathway (via cell cycle regulation and altered metabolism) as an active driver of growth variations in chicken. We recommend further functional characterisation and analysis of this pathway, in meat birds in particular, to further characterise variations in growth and performance.Thesis (Ph.D.) -- University of Adelaide, School of Animal and Veterinary Sciences, 201

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Excreta biomarkers in response to different gut barrier dysfunction models and probiotic supplementation in broiler chickens.

Increased intestinal permeability (IP) and inflammation are both linked with functionality of the intestinal barrier and in particular enterocytes. Currently, almost all assessment methods of the intestinal barrier function are invasive. The present study aimed to quantify selected proteins as novel biomarkers in excreta of broiler chickens to facilitate non-invasive assessment of gut barrier function using enzyme-linked immunosorbent assays (ELISA). It was further hypothesised that probiotics as feed additives may counteract gut barrier dysfunction. A 3 × 2 factorial arrangement of treatments was used with the main factors being gut barrier dysfunction models (control, rye-based diet, and dexamethasone-DEX) with and without probiotic supplementation (a three-strain Bacillus) using 72 male Ross 308 day-old chickens. Each of the 6 experimental treatments was replicated 12 times. On d 21 of age, fluorescein isothiocyanate dextran (FITC-d) uptake into serum was examined to test IP. Fresh excreta samples were collected on d 20. The biomarkers included alpha-1 antitrypsin (A1AT), intestinal fatty acid binding protein (I-FABP), lipocalin-2 (LCN2), fibronectin (FN), intestinal alkaline phosphatase (IAP), ovotransferrin (OVT) and superoxide dismutase [Cu-Zn] (SOD1). Only DEX increased (P<0.001) FITC-d passage to the blood on d 21 of age, indicating a greater IP. The excreta concentrations of A1AT, I-FABP and SOD1 were unaltered by the experimental treatments. DEX increased (P<0.05) FN concentration in excreta compared with control birds. Conversely, inclusion of rye in the diet reduced (P<0.05) FN but increased (P<0.001) OVT in excreta. Independently, DEX decreased IAP (P<0.05) in excreta compared with control and rye-fed birds. The excreta concentration of LCN2 tended (P = 0.086) to increase in birds injected by DEX. There was no demonstrable effect of probiotic addition on any of the studied parameters. Among the tested biomarkers, FN, IAP, and LCN2 revealed promise as biomarkers of intestinal barrier function quantified by ELISA kits

Evaluation of fatty acid metabolism and innate immunity interactions between commercial broiler, F1 layer × broiler cross and commercial layer strains selected for different growth potentials

Abstract Background The broiler industry has undergone intense genetic selection over the past 50 yr. resulting in improvements for growth and feed efficiency, however, significant variation remains for performance and growth traits. Production improvements have been coupled with unfavourable metabolic consequences, including immunological trade-offs for growth, and excess fat deposition. To determine whether interactions between fatty acid (FA) metabolism and innate immunity may be associated with performance variations commonly seen within commercial broiler flocks, total carcass lipid %, carcass and blood FA composition, as well as genes involved with FA metabolism, immunity and cellular stress were investigated in male birds of a broiler strain, layer strain and F1 layer × broiler cross at d 14 post hatch. Heterophil: lymphocyte ratios, relative organ weights and bodyweight data were also compared. Results Broiler bodyweight (n = 12) was four times that of layers (n = 12) by d 14 and had significantly higher carcass fat percentage compared to the cross (n = 6; P = 0.002) and layers (P = 0.017) which were not significantly different from each other (P = 0.523). The carcass and whole blood FA analysis revealed differences in the FA composition between the three groups indicating altered FA metabolism, despite all being raised on the same diet. Genes associated with FA synthesis and β-oxidation were upregulated in the broilers compared to the layers indicating a net overall increase in FA metabolism, which may be driven by the larger relative liver size as a percentage of bodyweight in the broilers. Genes involved in innate immunity such as TLR2 and TLR4, as well as organelle stress indicators ERN1 and XBP1 were found to be non-significant, with the exception of high expression levels of XBP1 in layers compared to the cross and broilers. Additionally there was no difference in heterophil: lymphocytes between any of the birds. Conclusions The results provide evidence that genetic selection may be associated with altered metabolic processes between broilers, layers and their F1 cross. Whilst there is no evidence of interactions between FA metabolism, innate immunity or cellular stress, further investigations at later time points as growth and fat deposition increase would provide useful information as to the effects of divergent selection on key metabolic and immunological processes

Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry

Stanley, D ORCiD: 0000-0001-7019-4726Immune function is influenced by the diversity and stability of the intestinal microbiota. A likely trade-off of immune function for growth has been demonstrated in heavier breeds of poultry that have been genetically selected for growth and feed efficiency traits. We investigated the expression of selected innate immune genes and genes encoding products involved in intestinal barrier function to determine whether function changes could be consistently linked to the phenotypic expression of feed conversion ratio (FCR), a common measure of performance within poultry broiler flocks. In addition, we compared individual cecal microbial composition with innate immune gene expression. Samples were utilised from two replicate trials termed P1E1 and P1E2. High (n = 12) and low (n = 12) performing birds were selected based on their individual FCR data from each replicate and combined for microbiota phylogenetic composition and immune gene expression analysis. Toll-like receptor 1 (TLR1La) and zonula occludens 1 (ZO1) were differentially expressed between high- and low-performing broilers. Several taxa were correlated with FCR; of these, unclassified YS2 and ZO1 were also positively correlated with each other. Interactions between taxa and differentially expressed innate immune genes between P1E1 and P1E2 were much greater compared to relationships between high- and low-performing birds. At the level of phylum, reciprocal correlations between tight junction proteins and Toll-like receptors with Bacteroidetes and Firmicutes were evident, as were correlations at the genus level. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature

Oregano: A potential prophylactic treatment for the intestinal microbiota

Stanley, D ORCiD: 0000-0001-7019-4726Prophylactic use of antibiotics in poultry diets has been identified as a problematic practice because of its potential to exacerbate the spread of antibiotic resistance to human pathogens. A range of countries have opted to completely ban the use of antibiotics in animal feed. The animal production industries are looking for alternative ways to effectively control pathogens while providing the performance benefits previously secured by antibiotics in feed. Here, we present evidence that oregano (Origanum vulgare) could be a potential alternative for pathogen control in the poultry industry. Broiler diets were supplemented with oregano powder (0%, 0.5%, 1%, and 2%) for six weeks. The capacity for pathogen control was estimated by microbiota profiling of the jejunum, ileum, and caecum content, and in the faeces, by 16S rRNA gene amplicon sequencing. The concentrations of short-chain fatty acids in the caecal content were also measured, as were villus/crypt parameters in the ileum. There were no differences among treatments in weight gain, feed intake, or the concentration of short-chain fatty acids. The height, width, and the surface area of villi in the ileum were not influenced by oregano addition. However, 1% and 2% of oregano produced a significant increase in the villus height to crypt depth ratio. There were no visible histopathological changes in the liver in control and treated groups. Although oregano had no significant effect on overall microbial diversity and gross composition, some specific genera, like Proteus, Klebsiella and Staphylococcus, which include known pathogens, were reduced in relative abundance by oregano treatment. Bifidobacterium, recognized as a beneficial and probiotic genus, was also suppressed by the oregano treatment. © 201

Nanoparticles of selenium as high bioavailable and non-toxic supplement alternatives for broiler chickens

Selenium is commonly used in the poultry industry as an additive in broiler feed to improve immunity and overall health. The selenium comes in different forms, inorganic and organic selenium, as sodium selenite and selenomethionine, respectively. This study proposes the use of nanoparticles of selenium (nanoSe) for improved delivery and absorption of the trace element while causing no toxicity. Previous studies have shown the success in utilizing nanoSe in broiler feed, with increased absorption and diffusion of material into organs and tissues, and increased antioxidant capacity. However, the mechanism of nanoSe conversion remains unknown, and the gut microbiota is believed to play a significant role in the process. The use of inorganic selenium in poultry feed demonstrated a lower bioavailability in breast (P ≤ 0.01) and duodenum tissue (P ≤ 0.05), and increased accumulation in organs involved in detoxification processes as compared to organic selenium and selenium nanoparticle supplementation. Histopathological analysis showed that nanoSe did not cause any damaging effects to the tissues analysed, revealing intact epithelial cells in the digestive system and neuronal bodies in brain tissue. The results indicate that nanoparticles of selenium operate a similar way to organic selenium and could potentially be used in poultry feed as a trace element additive

Feed supplementation with biochar may reduce poultry pathogens, including Campylobacter hepaticus, the causative agent of Spotty Liver Disease

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Increased global regulation and restrictions on the non-therapeutic use of antibiotics in the poultry industry means that there is a need to identify alternatives that prevent infection while still conveying the growth and performance benefits afforded by their use. Biochars are produced by the incomplete pyrolysis of organic materials, with reports of use as a feed supplement and activity against pathogenic bacteria. In the current study the dose-dependent effects of biochar dietary inclusion in layer diets at 1%, 2% and 4% w/w were investigated to determine a) the efficacy of biochar as an anti-pathogenic additive on the intestinal microbiota and b) the optimal inclusion level. Biochar inclusion for anti-pathogenic effects was found to be most beneficial at 2% w/w. Poultry pathogens such as Gallibacterium anatis and campylobacters, including Campylobacter hepaticus, were found to be significantly lower in biochar fed birds. A shift in microbiota was also associated with the incorporation of 2% w/w biochar in the feed in two large scale trials on two commercial layer farms. Biochar inclusion for anti-pathogenic effects was found to be most beneficial at 2% w/w. Differential effects of the timing of biochar administration (supplementation beginning at hatch or at point of lay) were also evident, with greater impact on community microbial structure at 48 weeks of age when birds were fed from hatch rather than supplemented at point of lay. © 2019 Willson et al