Genetic resilience in chickens against bacterial, viral and protozoal pathogens

Genetic characterization of infectious bursal disease virus strains with distinct VP2 amino acid profiles emerging in Pakistan

Infectious bursal disease (IBDV) poses a significant threat to the global poultry industry and causes major economic losses. This study presents the genetic profile of IBDV strains emerging in Pakistan, focusing on the VP2 amino acid profile. The effects of these changes on disease transmission, vaccine effectiveness, and overall chicken health are concerning. A meticulous analysis was carried out by isolating and clustering IBDV strains collected from Faisalabad district of Pakistan. The genetics of these viruses were evaluated by analyzing the VP2 gene, the main component of the virus. Importantly, our results reveal the existence of IBDV strains with unprecedented VP2 amino acid profiles, indicating genetic changes that may affect virulence and immunity. This study highlighted the changing IBDV landscape in Pakistan and underscores the importance of continued research and surveillance efforts. Understanding the genetic structure of these emerging diseases is essential for developing effective control strategies, including vaccine development and control. This also emphasized the need for international cooperation to reduce the spread of the new IBDV strains, which could significantly impact the poultry industry outside Pakistan.

Selection for Resilience in Livestock Production Systems

Selective breeding for improved animal resilience is becoming critical to increase the sustainability of production systems. Despite the existence of a genetic component for resilience, breeding for improved resilience has been limited by the absence of a consensus on its definition and quantifying method. In this work, we provide a review of (i) the definition of resilience and related concepts such as robustness, resistance, and tolerance; (ii) possible quantifying methods for resilience; (iii) its genetic background; and (iv) insights about its improvement through selective breeding. We suggest that a resilient animal may be defined as an individual that is able to cope with a perturbation(s) and rapidly bounce back to normal functioning if altered. Furthermore, since challenging conditions lead to trade-offs and, consequently, deviations between basic physiological functions, we suggest using these deviations as indicators for resilience. These resilience indicators may also be used as proxies to study the genetic determinism and background of resilience in livestock species. Finally, we discuss possible strategies to improve resilience and review the implementation of associated genetic markers for resilience indicators in selection schemes.

Avian Models for Human Carcinogenesis-Recent Findings from Molecular and Clinical Research

Birds, especially the chick and hen, have been important biomedical research models for centuries due to the accessibility of the avian embryo and the early discovery of avian viruses. Comprehension of avian tumor virology was a milestone in basic cancer research, as was that of non-viral genesis, as it enabled the discovery of oncogenes. Furthermore, studies on avian viruses provided initial insights into Kaposi's sarcoma and EBV-induced diseases. However, the role of birds in human carcinogenesis extends beyond the realm of virology research. Utilization of CAM, the chorioallantoic membrane, an easily accessible extraembryonic tissue with rich vasculature, has enabled studies on tumor-induced angiogenesis and metastasis and the efficient screening of potential anti-cancer compounds. Also, the chick embryo alone is an effective preclinical in vivo patient-derived xenograft model, which is important for the development of personalized therapies. Furthermore, adult birds may also closely resemble human oncogenesis, as evidenced by the laying hen, which is the only animal model of a spontaneous form of ovarian cancer. Avian models may create an interesting alternative compared with mammalian models, enabling the creation of a relatively cost-effective and easy-to-maintain platform to address key questions in cancer biology.

The effect of coffee husks used as pellet bedding material on the intestinal barrier, immune-related gene expression and microbiota composition in the broiler chicken caecum

Introduction

Using coffee husks as waste material for bedding contributes to sustainable development. A sustainable choice of bedding has also, however, to be a safe choice for poultry. The study analysed immune-related gene expression in the intestinal mucosa and indicator bacteria in caecal content collected from broiler chickens bedded on material with coffee husk addition.

Material and Methods

One-day-old Ross 308 chickens were divided into four groups of 10 birds each in five replicates: C, the control group kept on wheat straw bedding; CH10, a group kept on bedding of 10% coffee husks and 90% wheat straw; CH25, a group kept on bedding of 25% husks and 75% straw; and CH50, a group kept on bedding of 50% husks and 50% straw. After 42 days, the birds were slaughtered, the caecal mucosae were removed for RNA isolation and the caecal content was collected for bacterial DNA isolation. The expression of genes involved in intestinal immune response and host organism defence and the relative abundance of indicator bacteria were analysed.

Results

Upregulation of the expression of genes related to the immune response and intestinal tightness was correlated with an increase in the percentage of coffee husks in the pellet. Coffee husk pellets at 50% bedding content caused a significant numerical increase in Bifidobacterium and a statistically significant increase in Lactobacillus. A significant reduction in E. coli bacteria was also demonstrated in this group. Coffee husk pellets at all content percentages resulted in a statistically significant diminution of the level of Streptococcus bacteria.

Conclusion

The addition of coffee husks to poultry litter effects beneficial changes in the expression of genes related to intestinal health and the caecal bacterial profile.

Advancement of animal and poultry nutrition: Harnessing the power of CRISPR-Cas genome editing technology

CRISPR-associated proteins and clustered regularly interspaced short palindromic repeats (CRISPR-Cas) technology has emerged as a groundbreaking advancement in animal and poultry nutrition to improve feed conversion efficiency, enhance disease resistance, and improve the nutritional quality of animal products. Despite significant advancements, there is a research gap in the systematic understanding and comprehensive use of the CRISPR-Cas method in animal and poultry nutrition. The purpose of this study is to elucidate the latest advancements in animal and poultry nutrition through CRISPR-Cas genome editing technology, focusing on gene manipulation in metabolism, immunity, and growth. Following preferred reporting items in meta-analysis and systematic reviews guidelines, we conducted a systematic search using several databases, including Scopus, PubMed, and Web of Science, until May 2024, and finally, we included a total of 108 articles in this study. This article explores the use of the CRISPR-Cas system in the advancement of feed additives like probiotics and enzymes, which could reduce the use of antibiotics in animal production. Furthermore, the article discusses ethical and regulatory issues related to gene editing in animal and poultry nutrition, including concerns about animal welfare, food safety, and environmental impacts. Overall, the CRISPR-Cas system holds substantial promise to overcome the challenges in modern animal agriculture. By enriching the nutritional quality of animal products, increasing disease resistance, and improving feed efficiency, it offers sustainable and cost-effective solutions that can revolutionize animal and poultry nutrition.

The Immunological Basis for Vaccination

Vaccination is crucial for health protection of poultry and therefore important to maintaining high production standards. Proper vaccination requires knowledge of the key players of the well-orchestrated immune system of birds, their interdependence and delicate regulation, and, subsequently, possible modes of stimulation through vaccine antigens and adjuvants. The knowledge about the innate and acquired immune systems of birds has increased significantly during the recent years but open questions remain and have to be elucidated further. Despite similarities between avian and mammalian species in their composition of immune cells and modes of activation, important differences exist, including differences in the innate, but also humoral and cell-mediated immunity with respect to, for example, signaling transduction pathways, antigen presentation, and cell repertoires. For a successful vaccination strategy in birds it always has to be considered that genotype and age of the birds at the time point of immunization as well as their microbiota composition may have an impact and may drive the immune reactions into different directions. Recent achievements in the understanding of the concept of trained immunity will contribute to the advancement of current vaccine types helping to improve protection beyond the specificity of an antigen-driven immune response. The fast developments in new omics technologies will provide insights into protective B- and T-cell epitopes involved in cross-protection, which subsequently will lead to the improvement of vaccine efficacy in poultry.

A critical assessment of the cellular defences of the avian respiratory system: are birds in general and poultry in particular relatively more susceptible to pulmonary infections/afflictions?

In commercial poultry farming, respiratory diseases cause high morbidities and mortalities, begetting colossal economic losses. Without empirical evidence, early observations led to the supposition that birds in general, and poultry in particular, have weak innate and adaptive pulmonary defences and are therefore highly susceptible to injury by pathogens. Recent findings have, however, shown that birds possess notably efficient pulmonary defences that include: (i) a structurally complex three-tiered airway arrangement with aerodynamically intricate air-flow dynamics that provide efficient filtration of inhaled air; (ii) a specialised airway mucosal lining that comprises air-filtering (ciliated) cells and various resident phagocytic cells such as surface and tissue macrophages, dendritic cells and lymphocytes; (iii) an exceptionally efficient mucociliary escalator system that efficiently removes trapped foreign agents; (iv) phagocytotic atrial and infundibular epithelial cells; (v) phagocytically competent surface macrophages that destroy pathogens and injurious particulates; (vi) pulmonary intravascular macrophages that protect the lung from the vascular side; and (vii) proficiently phagocytic pulmonary extravasated erythrocytes. Additionally, the avian respiratory system rapidly translocates phagocytic cells onto the respiratory surface, ostensibly from the subepithelial space and the circulatory system: the mobilised cells complement the surface macrophages in destroying foreign agents. Further studies are needed to determine whether the posited weak defence of the avian respiratory system is a global avian feature or is exclusive to poultry. This review argues that any inadequacies of pulmonary defences in poultry may have derived from exacting genetic manipulation(s) for traits such as rapid weight gain from efficient conversion of food into meat and eggs and the harsh environmental conditions and severe husbandry operations in modern poultry farming. To reduce pulmonary diseases and their severity, greater effort must be directed at establishment of optimal poultry housing conditions and use of more humane husbandry practices.

RNA-Seq Profiling between Commercial and Indigenous Iranian Chickens Highlights Differences in Innate Immune Gene Expression

The purpose of the current study was to examine transcriptomic-based profiling of differentially expressed innate immune genes between indigenous and commercial chickens. In order to compare the transcriptome profiles of the different chicken breeds, we extracted RNA from blood samples of the Isfahan indigenous chicken (as indigenous) and Ross broiler chicken (as commercial) breeds. RNA-Seq yielded totals of 36,763,939 and 31,545,002 reads for the indigenous and commercial breeds, respectively, with clean reads then aligned to the chicken reference genome (Galgal5). Overall, 1327 genes were significantly differentially expressed, of which 1013 genes were upregulated in the commercial versus the indigenous breed, while 314 were more highly expressed in the indigenous birds. Furthermore, our results demonstrated that the SPARC, ATP6V0D2, IL4I1, SMPDL3A, ADAM7, TMCC3, ULK2, MYO6, THG1L and IRG1 genes were the most significantly expressed genes in the commercial birds and the PAPPA, DUSP1, PSMD12, LHX8, IL8, TRPM2, GDAP1L1, FAM161A, ABCC2 and ASAH2 genes were the most significant in the indigenous chickens. Of notable finding in this study was that the high-level gene expressions of heat-shock proteins (HSPs) in the indigenous breeds could serve as a guideline for future genetic improvement. This study identified genes with breed-specific expression, and comparative transcriptome analysis helped understanding of the differences in underlying genetic mechanisms between commercial and local breeds. Therefore, the current results can be used to identify candidate genes for further breed improvement.