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Data and R scripts for the paper:Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens. Data includes the phyloseq RDS for the 16S rRNA v3v4 sequencing data and its metadata. Analysis scripts as used for the paper for both the modeling and the microbiome. See README for more details. Links: NCBI SRA BioProject:PRJNA948179 Paper doi: Abstract paper: Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens Natcha Dankittipong, Jesse B. Alderliesten, Jan Van den Broek, M. Anita Dame-Korevaar, Michael S. M. Brouwer, Francisca C. Velkers, Alex Bossers, Clazien J. de Vos, Jaap A. Wagenaar, J. Arjan Stegeman, Egil A. J. Fischer The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria similar to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistant E. coli. A total of 180 Ross 308 broiler chickens were distributed on the day of hatch (day 0) over 12 pens. On day 5, half of the chickens in each pen were orally inoculated with 5·102 colony-forming units of CPE, ESBL, or chloramphenicol-resistant E. coli (catA1). Amoxicillin drinking water treatment was given twice daily in 6 of the 12 pens from days 2 to 6 to evaluate the effect of antibiotic treatment on the transmission rates. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of the E. coli strains. E. coli can survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates. The transmission rates of CPE were 52 – 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or between the E. coli strains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2 to 6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect. Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.

Fat-associated lymphoid clusters (FALCs) are novel lymphoid tissues that have been reported in the mesenteric and mediastinal fat tissue of mouse and human. It plays role in the progression of respiratory and intestinal inflammation and parasitic infestations. However, their occurrence in the chicken air sacs and mesenteric adipose tissue has not yet been identified. Here we investigated the occurrence and distribution of FALCs in the air sacs (cervical, clavicular, thoracic, and abdominal) and mesenteric adipose tissue of healthy chicken. The latter air sacs and mesentery were immediately harvested after anesthesia and cutting the chicken heads then fixed in 4% paraformaldehyde fixative solution for histopathological examination. The degree of FALCs development among different specimens was measured and statistically analyzed. Our results revealed lymphoid clusters associating with the adipose tissues in mesentery, and air sacs (clavicular, thoracic, and abdominal), but not the cervical one. Interestingly, the thoracic air sacs showed significant higher FALCs size in comparison to that of other air sac types and the mesentery. Our findings suggested other possible immunological role of the air sacs and mesentery that could have impact on the progression of air sacculitis and mesenteritis- associate diseases. However, further investigations are required for clarification of air sacs and mesenteric FALCs in the progressions of respiratory and digestive tract diseases.

The health and productivity of broiler chickens are related to their intestinal microbiota, which may be influenced by supplemented feed components. This trial intended to evaluate the effects of a dietary mixture of essential oils from oregano (Origanum vulgare ssp. hirtum), sage (Salvia triloba L.), and lavender (Lavandula angustifolia L.) on broiler chicken growth performance, intestinal microbiota, intestinal morphology, and meat chemical composition and oxidative stability. A total of 288 one-day-old male Ross-308 chicks were randomly assigned to four treatments with six replicate pens (12 chicks per pen). The chicks of the control treatment were fed typical commercial maize and soybean meal rations in mash form. The rations of the other three treatments were supplemented with a mixture of essential oils at 100, 200, and 400 mg/kg, respectively. At the end of the trial (day 42), tissue samples were collected for analysis. Major bioactive components of the three essential oils were identified by gas chromatography-mass spectrometry. Essential oil supplementation increased the radical scavenging capacity and the total phenolic content of the feeds. Performance parameters (weight gain, feed intake, feed conversion ratio, European production efficiency factor) were not affected significantly by the supplementation. Intestinal microflora populations (determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry) were modified significantly in both the cecum and the jejunum. Breast and thigh meat oxidative stability under refrigerated storage was improved significantly. Additional research is required to elucidate the potential synergistic effects of dietary mixtures of essential oils.

The poultry sector is considered to be one of the most industrialized sectors of livestock production. Although the livestock sector contributes the 14.5% of total anthropogenic greenhouse gas (GHG) emissions, less attention has been paid in the respective emissions of the poultry sector compared to other farmed animals such as ruminants. The aim of the study was to estimate the carbon footprint of the poultry sector (layers, broilers, and backyards) in the Greek territory during the last 60 years as a means of exploring further mitigation strategies. Tier 2 methodology was used to estimate GHG emissions. Different mitigation scenarios related to changes in herd population, feeds, and manure management were examined. GHG emissions showed an increased trend over time. The different scenarios explored showed moderate to high mitigating potential depending on the parameters that were changed. Changes in manure management or diet revealed to have a higher potential to eliminate GHG emissions. Changes in population numbers showed a low mitigating potential. However, if mortality could be improved within industrialized farming systems, then it could be an indirect increase in product quantities with a slight increase in emissions. Therefore, depending on national priorities, the sector could improve its environmental impact by targeting aspects related to husbandry/management practices.

Salmonella Enteritidis is the main serotype responsible for human salmonellosis in the European Union. One of the main sources of Salmonella spp. in the food chain are poultry products, such as eggs or chicken meat. In recent years, molecular methods have become an alternative to culture dependent methods for the rapid screening of Salmonella spp. In this work, the strain S. Enteritidis S1400, and previously isolated and characterized bacteriophage PVP-SE2, were used to develop and evaluate a same-day detection method combining Phage Amplification and Loop-mediated isothermal amplification (PA-LAMP) to specifically detect viable S. Enteritidis in chicken breast. This method is based on the detection of the phage DNA rather than bacterial DNA. The virus is added to the sample during pre-enrichment in buffered peptone water, where it replicates in the presence of viable S. Enteritidis. The detection of phage DNA allows, on the one hand to detect viable bacteria, since viruses only replicate in them, and on the other hand to increase the sensitivity of the method since for each infected S. Enteritidis cell, hundreds of new viruses are produced. Two different PA-LAMP detection strategies were evaluated, a real time fluorescence and a naked-eye detection. The present method could down to 0.2 fg/L of pure phage DNA and a concentration of viral particles of 2.2 log PFU/mL. After a short Salmonella recovery step of 3 h and a co-culture of 4 h of the samples with phage particles, both real-time fluorescence and naked-eye method showed a LoD95 of 6.6 CFU/25 g and a LoD50 of 1.5/25 g in spiked chicken breast samples. The entire detection process, including DNA extraction and LAMP analysis, can be completed in around 8 h. In the current proof-of-concept, the novel PA-LAMP obtained comparable results to those of the reference method ISO 6579, to detect Salmonella Enteritidis in poultry meat., Dr. Alexandre Lamas was funded by a postdoctoral fellowship from Xunta de Galicia (Axudas de apoio a étapa de formación posdoutoral IN606B (Modalidade A)). Dr. Alejandro Garrido-Maestu acknowledges funding from the Fundação para a Ciência e Tecnologia through the Scientific Employment Stimulus Program (2021.02810.CEECIND)., info:eu-repo/semantics/publishedVersion

application/pdf, In recent years, the market share for cage-free eggs has gradually increased. Because commercially available cage-free eggs are often produced not only by several housing systems but also with different feed crude protein (CP) levels, there are combined effects of feed and housing systems between cage-free and cage eggs. Therefore, using field data, this study aimed to determine the combined effects of feed and housing systems on egg traits and yolk and albumen amino acids in table eggs. Brown layers (n = 40) at the middle laying stage under two feed and housing systems (cage, CP 15.5% diet; barn, CP 17.0% diet) were used. One-way analysis of variance and Pearson’s correlation analysis were used to evaluate 10 egg traits, 19 yolk amino acid traits, and 20 albumen amino acid traits. We observed significant effects of feed and housing on two egg traits (yolk weight and eggshell color redness), 16 yolk amino acids (Asp, Glu, Asn, Ser, Gln, His, Arg, Thr, Ala, Tyr, Met, Cys, Ile, Leu, Phe, and Lys), and 14 albumen amino acids (Asp, Asn, Ser, Gln, Gly, His, Arg, Thr, Ala, Val, Met, Cys, Ile, and Leu). This study revealed that eggs from the barn system (CP 17.0%) contained higher levels of free amino acids in 15 yolk and nine albumen amino acid traits. Phenotypic correlations among the 49 egg traits indicated similar correlation patterns in both systems, which implies that the balance of free amino acid content in yolk and albumen is similar in each system. Although some potential confounding factors may be present for comparing egg content between cage (CP 15.5%) and barn (CP 17.0%) systems, this study suggests that commercially available cage-free eggs may be different from cage eggs not only in external egg traits but also yolk and albumen amino acid traits.

As part of a program to reduce numbers of the human pathogen Campylobacter on retail chickens, 22 broiler processing lines, representing more than 90% of UK production, were characterized by enumerating Campylobacter on pooled neck skins after exsanguination, scalding, defeathering, evisceration, crop removal, inside-outside washing, and air-chilling stages of processing. Sixteen of the processing lines investigated showed significant (P < 0.05) reductions in Campylobacter numbers because of carcass scalding. However, in all of these lines, the following defeathering stage caused a significant increase in Campylobacter contamination that effectively negated the reductions caused by scalding. On four processing lines, primary chilling also caused a significant reduction in numbers of Campylobacter. On three lines, there was a significant microbiological benefit from inside-outside washing. The stages where Campylobacter numbers were reduced require further investigation to determine the specific mechanisms responsible so that the observed pathogen reductions can be optimized and then more widely implemented. The transfer of up to 4 log CFU Campylobacter per g of neck skin from a colonized flock to a following uncolonized flock was observed. Cross-contamination was substantial and still detectable after 5,000 carcasses from an uncolonized flock had been processed. Numbers of Campylobacter recovered from the uncolonized flocks were highest on the first of the uncolonized birds to pass along the line, and in general, the numbers declined as more uncolonized birds were processed. Air sampling recovered low numbers at the processing stages monitored, indicating that airborne transmission was unlikely to be the primary transfer mechanism operating for cross-contamination between flocks.

Lameness or leg weakness is the main cause of poor poultry welfare and serious economic losses in meat-type poultry production worldwide. Disorders related to the legs are often associated with multifactorial aetiology which makes diagnosis and proper treatment difficult. Among the infectious agents, bacteria of genus Staphylococcus are one of the most common causes of bone infections in poultry and are some of the oldest bacterial infections described in poultry. Staphylococci readily infect bones and joints and are associated with bacterial chondronecrosis with osteomyelitis (BCO), spondylitis, arthritis, tendinitis, tenosynovitis, osteomyelitis, turkey osteomyelitis complex (TOC), bumblefoot, dyschondroplasia with osteomyelitis and amyloid arthropathy. Overall, 61 staphylococcal species have been described so far, and 56% of them (34/61) have been isolated from clinical cases in poultry. Although Staphylococcus aureus is the principal cause of poultry staphylococcosis, other Staphylococcus species, such as S. agnetis, S. cohnii, S. epidermidis, S. hyicus, S. simulans, have also been isolated from skeletal lesions. Antimicrobial treatment of staphylococcosis is usually ineffective due to the location and type of lesion, as well as the possible occurrence of multidrug-resistant strains. Increasing demand for antibiotic-free farming has contributed to the use of alternatives to antibiotics. Other prevention methods, such as better management strategies, early feed restriction or use of slow growing broilers should be implemented to avoid rapid growth rate, which is associated with locomotor problems. This review aims to summarise and address current knowledge on skeletal disorders associated with Staphylococcus spp. infection in poultry.

Avian-derived IgY is thought to be the best therapy for scorpion bites concerning low-level side effects. The present study analyzed a hypothesis about the neutralization of scorpion venom Androcotonus australis through antibodies produced in the egg yolks of chickens. The venom used for inoculation was obtained from Androctonus australis (yellow fat-tailed scorpion) from southern Punjab, Pakistan. The lethal dose of LD50 against scorpion venom was calculated in chickens and mice. Safe doses were given to egg-laying chickens to produce IgY antibodies. The antivenom IgY antibodies were extracted from the egg yolks of immunized chicken using the polyethylene glycol (PEG) method. Moreover, IgY was confirmed through sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and the Ouchterlony double immunodiffusion assay test. The antibody titers were evaluated by the enzyme-linked immunosorbent assay (ELISA). The neutralisation capacity of extracted anti-scorpion antibodies was tested on mice. The calculated LD50 of scorpion venom for chicken and mice was 4 mg/kg and 2.5 mg/kg, respectively. SDS-PAGE and Ouchterlony double immunodiffusion confirmed the presence of IgY against scorpion venom. The maximum titer value of specific IgY produced against scorpion venom was 3.5 ug/ml. A concentration of 220 ul/LD50 was effective to neutralize 1 mg of scorpion venom. It is suggested that IgY obtained from egg yolks is safe against targeted venom and can be used as an effective alternative to equine IgG antibodies against scorpion envenoming. RESUMO: Acredita-se que a IgY derivada de aves seja a melhor terapia para picadas de escorpião em relação aos efeitos colaterais. O presente estudo teve como objetivo analisar uma hipótese sobre a neutralização do veneno do escorpião Androcotonus australis através de anticorpos produzidos na gema de ovos de galinhas. O veneno usado para inoculação foi obtido de Androctonus australis (escorpião amarelo de cauda gorda) do sul de Punjab, Paquistão. A dose letal de LD50 contra veneno de escorpião foi calculada em galinhas e camundongos. Doses seguras foram dadas a galinhas poedeiras para produzir anticorpos IgY. Os anticorpos antiveneno IgY foram extraídos das gemas de ovos de galinhas imunizadas pelo método do polietilenoglicol (PEG). Além disso, a IgY foi confirmada por eletroforese em gel de poliacrilamida e dodecil sulfato de sódio (SDS-PAGE) e pelo teste de imunodifusão dupla de Ouchterlony. Os títulos de anticorpos foram avaliados pelo ensaio imunoenzimático (ELISA). A capacidade de neutralização dos anticorpos anti-escorpião extraídos foi testada em camundongos. A LD50 calculada do veneno de escorpião para galinhas e camundongos foi de 4 mg/kg e 2,5 mg/kg, respectivamente. SDS-PAGE e imunodifusão dupla Ouchterlony confirmaram a presença de IgY contra veneno de escorpião. O valor máximo do título de IgY específico produzido contra veneno de escorpião foi de 3,5 ug/ml. Uma concentração de 220 ul/LD50 foi considerada eficaz para neutralizar 1 mg de veneno de escorpião. Sugere-se que a IgY obtida da gema do ovo seja segura contra o veneno direcionado e possa ser usada como uma alternativa eficaz aos anticorpos IgG equinos contra o envenenamento por escorpiões.

A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.

Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as IκBα, STAT1/STAT3, GSK-3β, or p53) and related key signaling pathways (such as NF-κB, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.

With the practice of a successful livestock industry using antibiotics, which has continued for more than five decades, researchers have long been interested in finding alternatives to antibiotics for poultry production. Probiotics can potentially reduce enteric diseases in livestock and enhance their productivity. The aim of this study was to isolate putative probiotics from camel milk and test them against Salmonella infection as well as host immune development. Thirteen different isolates were obtained from six different camel milk samples from dairy farms in Saudi Arabia. Three of the six isolates (PM1, PM2, PM3, PM4, PM5, and PM6) that showed Gram-positive characters reacted negatively to catalase and hemolytic assays. PM1, PM5, and PM6 showed significant nonpolar surface properties (>51% hydrophobic) and potent antimicrobial activities against avian pathogens, namely S. enterica, S. typhi, S. aureus, and E. coli. PM5 exhibited substantial probiotic traits; therefore, further focus was given to it. PM5 was identified as Bacillussubtilis OQ913924 by the 16S rRNA sequencing method and showed similarity matrix > 99%. An in vivo chicken model was used to access the health benefits of probiotics. After salmonella infection, the mucosal immune response was significantly increased (p < 0.01), and none of the challenge protocols caused mortality or clinical symptoms after infection in intestinal contents. S. enterica organ infiltration in the spleen, thymus, and small intestine was significantly reduced in the B. subtilis PM5-fed chickens. The S. enterica load in chicken feces was reduced from CFU 7.2 to 5.2 in oral-fed B. subtilis PM5-fed chickens. Probiotic-fed chickens showed buffered intestinal content and positively regulated the level of butyric acid (p < 0.05), and intestinal interleukin 1 beta (IL1-β), C-reactive protein (CRP), and interferon gamma (IFN-γ) levels were reduced (p < 0.05). In addition, B. subtilis PM5 showed significant binding to peritoneal macrophages cells and inhibited S. enterica surface adhesion, indicating co-aggregation of B. subtilis PM5 in macrophage cells. It could be concluded that supplementation with probiotics can improve the growth performance of broilers and the quality of broiler chickens against enteric pathogens. The introduction of this probiotic into the commercial poultry feed market in the near future may assist in narrowing the gap that now exists between chicken breeding and consumer demand.

Providing light during incubation is being investigated as a method to improve welfare in later life in poultry. This incubation method would more closely approximate chicken natural environment compared to the current incubation in darkness. Previous studies showed promising results of light during incubation on broiler welfare, but little is known about effects of light during incubation on laying hens. Especially, information about its effects on hatching characteristics (hatch time, hatchability, chick quality, body weight and embryonic age of death) is scarce and requires investigation in both white and brown egg layers. In the current study, Dekalb White (DW) and ISA Brown (ISA) eggs were incubated in complete darkness (dark) or in a light:dark cycle of 12L:12D throughout incubation (light), resulting in four treatment groups: DW-dark, DW-light, ISA-dark, and ISA-light. In the light treatments, green LEDs of 520nm wavelength were used, at an intensity of 400lux. First, light transmission through the eggshell was measured through 27 eggs. Then, an analysis of the effects of light during incubation on hatching characteristics was performed on 711 chicks in two consecutive experimental rounds. Light transmission was higher through white eggshells than through brown eggshells (N=27,p< 0.001). Light during incubation had no effects on hatching characteristics (N=711,p≥0.1). Despite the difference of light transmission through eggshell between hybrids, there was no interaction between incubation treatment and hybrid on hatching characteristics (N=471,p≥0.06). Hatch time was longer and navel quality was better in DW than in ISA, while body weight and embryonic age of death were lower in DW than in ISA (allp< 0.001). Males and females had similar chick quality scores except for the beak quality, which was better for males (N=486,p=0.003). To conclude, green light during incubation did not negatively affect hatching characteristics in either DW nor ISA laying hen hybrids. Future research should therefore focus on its potential benefits for laying hen welfare.

application/pdf, Many countries have gradually shifted to animal welfare-friendly housing systems for egg layers. However, there is still no consensus among researchers on whether the housing system affects egg quality traits. Therefore, this study aimed to determine the effects of housing systems on egg traits and free amino acid contents of albumen and yolk using two types of housing systems, the conventional cage (cage) system and a floor rearing (litter) system. Tosa-jidori (n = 20) hens were divided into two groups. Experiments during the 7 weeks were performed twice by switching the housing systems (first and second stages). One-way analysis of variance was used to evaluate the effects of housing systems on body weight gain, egg traits, albumen and yolk amino acid contents, and fecal corticosterone. We observed significant housing effects in body weight gain, eggshell weight, yolk weight, eggshell thickness, eggshell lightness, and several albumen amino acids (A_Gln, A_His, A_Met, A_Cys, A_Lys, A_Asp, A_Glu, A_Ser, A_Thr, A_Ala, A_Pro, and A_Phe). Notably, a robust effect was seen in eggshell lightness, even after switching housing systems. These results suggest that eggshell lightness and several egg traits, including albumen amino acid contents, can be changed by using the different housing systems.

Many countries have gradually shifted to animal welfare-friendly housing systems for egg layers. However, there is still no consensus among researchers on whether the housing system affects egg quality traits. Therefore, this study aimed to determine the effects of housing systems on egg traits and free amino acid contents of albumen and yolk using two types of housing systems, the conventional cage (cage) system and a floor rearing (litter) system. Tosa-jidori (n = 20) hens were divided into two groups. Experiments during the 7 weeks were performed twice by switching the housing systems (first and second stages). One-way analysis of variance was used to evaluate the effects of housing systems on body weight gain, egg traits, albumen and yolk amino acid contents, and fecal corticosterone. We observed significant housing effects in body weight gain, eggshell weight, yolk weight, eggshell thickness, eggshell lightness, and several albumen amino acids (A_Gln, A_His, A_Met, A_Cys, A_Lys, A_Asp, A_Glu, A_Ser, A_Thr, A_Ala, A_Pro, and A_Phe). Notably, a robust effect was seen in eggshell lightness, even after switching housing systems. These results suggest that eggshell lightness and several egg traits, including albumen amino acid contents, can be changed by using the different housing systems.

The landfill environment in Palembang City produces various types of waste so that people keep free-range chickens around the environment, which is potentially harmful to livestock health. This study aims to determine the color morphology of the internal organs (liver and heart) and the relationship between body weight and organ weight. The number of free-range chickens used was 30, with one year. The morphological description of organ color was carried out by direct observation, and sampling was carried out by weighing free-range chickens body weight and organ weight. This study used the Pearson correlation statistical test, and secondary data was collected on waste data in the landfill environment. The results showed that the relationship between body weight and liver weight was 0.694, and the correlation value between body weight and heart weight was 0.663 in native chickens in the landfill environment. The results of the two values have a strong correlation interpretation, which means that when the chicken's body weight increases, the weight of the liver and heart of the chicken will also increase. The liver is faded red with normal size in native chickens in the landfill environment in the morphological picture. While the color of the heart is red, and the size is normal.

There are two types of secretory cells in the chicken bursa of Fabricius (BF): (a) interfollicular epithelial cells (IFE), and (b) bursal secretory dendritic cells (BSDC) in the medulla of bursal follicles. Both cells produce secretory granules, and the cells are highly susceptible to IBDV vaccination and infection. Before and during embryonic follicular bud formation, an electron-dense, scarlet-acid fuchsin positive substance emerges in the bursal lumen, the role of which is unknown. In IFE cells, IBDV infection may induce rapid granular discharge, and in several cells, peculiar granule formation, which suggests that the glycosylation of protein is injured in the Golgi complex. In control birds, the discharged BSDC granules appear in membrane-bound and subsequently solubilized, fine-flocculated forms. The solubilized, fine-flocculated substance is Movat-positive and can be a component of the medullary microenvironment, which prevents the medullary B lymphocytes from nascent apoptosis. Vaccination interferes with the solubilization of the membrane-bound substance, resulting in: (i) aggregation of a secreted substance around the BSDC, and (ii) solid lumps in the depleted medulla. The non-solubilized substance is possibly not “available” for B lymphocytes, resulting in apoptosis and immunosuppression. In IBDV infection, one part of the Movat-positive Mals fuse together to form a medullary, gp-containing “cyst”. The other part of Mals migrate into the cortex, recruiting granulocytes and initiating inflammation. During recovery the Movat-positive substance appears as solid, extracellular lumps between the cells of FAE and Mals. Possibly the Mals and Movat-positive extracellular lumps glide into the bursal lumen via FAE to eliminate cell detritus from the medulla.

Liver diseases seriously challenge the health of chickens raised on scaled farms and cause tremendous economic losses to farm owners. The causative agents for liver diseases are still elusive, even though various pathogens, such as the hepatitis E virus, have been reported. In the winter of 2021, a liver disease was observed on a chicken farm in Dalian, China, which increased chicken mortality by up to 18%. We conducted panvirome profiling of the livers, spleens, kidneys, and recta of 20 diseased chickens. The viromic results revealed coinfection of multiple viruses, including pathogenic ones, in these organs. The viruses were highly identical to those detected in other provinces, and the vaccine and field strains of avian encephalomyelitis virus (AEV) and chicken infectious anemia virus (CIAV) cocirculated on the farm. In particular, the liver showed higher abundance of AEV and multiple fowl adenoviruses than other organs. Furthermore, the liver also contracted avian leukemia virus and CIAV. Experimental animals with infected liver samples developed minor to medium lesions of the liver and showed a virus abundance profile for AEV across internal organs similar to that in the original samples. These results suggest that coinfection with multiple pathogenic viruses influences the occurrence and development of infectious liver disease. The results also highlight that strong farm management standards with strict biosafety measures are needed to minimize the risk of pathogenic virus introduction to the farm.

Growing evidence has shown the involvement of the gut–liver axis in lipogenesis and fat deposition. However, how the gut crosstalk with the liver and the potential role of gut–liver crosstalk in the lipogenesis of chicken remains largely unknown. In this study, to identify gut–liver crosstalks involved in regulating the lipogenesis of chicken, we first established an HFD-induced obese chicken model. Using this model, we detected the changes in the metabolic profiles of the cecum and liver in response to the HFD-induced excessive lipogenesis using ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) analysis. The changes in the gene expression profiles of the liver were examined by RNA sequencing. The potential gut–liver crosstalks were identified by the correlation analysis of key metabolites and genes. The results showed that a total of 113 and 73 differentially abundant metabolites (DAMs) between NFD and HFD groups were identified in the chicken cecum and liver, respectively. Eleven DAMs overlayed between the two comparisons, in which ten DAMs showed consistent abundance trends in the cecum and liver after HFD feeding, suggesting their potential as signaling molecules between the gut and liver. RNA sequencing identified 271 differentially expressed genes (DEGs) in the liver of chickens fed with NFD vs. HFD. Thirty-five DEGs were involved in the lipid metabolic process, which might be candidate genes regulating the lipogenesis of chicken. Correlation analysis indicated that 5-hydroxyisourate, alpha-linolenic acid, bovinic acid, linoleic acid, and trans-2-octenoic acid might be transported from gut to liver, and thereby up-regulate the expression of ACSS2, PCSK9, and CYP2C18 and down-regulate one or more genes of CDS1, ST8SIA6, LOC415787, MOGAT1, PLIN1, LOC423719, and EDN2 in the liver to enhance the lipogenesis of chicken. Moreover, taurocholic acid might be transported from the gut to the liver and contribute to HFD-induced lipogenesis by regulating the expression of ACACA, FASN, AACS, and LPL in the liver. Our findings contribute to a better understanding of gut–liver crosstalks and their potential roles in regulating chicken lipogenesis.

The kruppel-like factor (KLF) gene family is a group of transcription factors containing highly conserved zinc-finger motifs, which play a crucial role in cell proliferation and differentiation. Chicken has been widely used as a model animal for analyzing gene function, however, little is known about the function of the KLF gene family in chickens. In this study, we performed genome-wide studies of chicken KLF genes and analyzed their biological and expression characteristics. We identified 13 KLF genes from chickens. Our phylogenetic, motif, and conserved domain analyses indicate that the KLF gene family has remained conserved through evolution. Synteny analysis showed the collinear relationship among KLFs, which indicated that they had related biomolecular functions. Interaction network analysis revealed that KLFs worked with 20 genes in biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that KLF2 was involved in Apelin and Forkhead Box O (FOXO) signaling pathways. Moreover, qPCR showed that 13 KLF genes were expressed in the nine selected tissues and displayed various gene expression patterns in chickens. RNA-seq showed that KLF3 and KLF10 genes were differentially expressed in the normal and high-fat diet fed groups, and KLF4, KLF5, KLF6, KLF7, KLF9, KLF12, and KLF13 genes were differentially expressed between undifferentiated and differentiated chicken preadipocytes. Besides, RNA-seq also showed that KLF genes displayed different expression patterns in muscle at 11 and 16 embryonic days old, and in 1-day-old chickens. These results indicated that the KLF genes were involved in the development of muscle and fat in chickens. Our findings provide some valuable reference points for the subsequent study of the function of KLF genes.

Plan de negocios para un proyecto agropecuario de explotación avicola en el municipio de Toca, Boyaca Business plan for a poultry farming project in the municipality of Toca, Boyaca Especialista en Gerencia de Empresas Agropecuarias Especialización

Commercial poultry diets are deficient in omega-3 fatty acids (n-3 FA) essential for embryonic brain development. Feeding n-3 FA to broiler and layer breeder chickens may directly benefit them and could increase their offspring's health, welfare, and productivity. This thesis aimed to assess the effects of maternal feeding n-3 FA on the brain size and n-3 FA concentration, cognition, and fearfulness of layer and broiler offspring. Ross 708 broiler breeders were fed a control (n-6 to n-3 ratio 26.1:1) or flaxseed (4.81:1) diet during the rearing and laying period, resulting in four maternal diet combinations (control-control, control-flaxseed, flaxseed-control, flaxseed-flaxseed). Two strains of layer breeders, ISA Brown and Shaver White, were also fed a control (7.56:1) or flaxseed (5.31:1) diet. Layer and broiler offspring were assessed for brain size and docosahexaenoic acid (DHA) concentration, performance in two types of learning tests (T-maze and discrimination tasks), fear response to a novel object and social isolation. Although maternal feeding of n-3 supplemented diets resulted in significantly greater brain-to-body weight ratios in broiler offspring and decreased brain n-6: n-3 FA ratio in layer offspring, we found little evidence that maternal flaxseed diets resulted in differences in offspring cognition or fearfulness. There were sex-specific effects of maternal diet on broiler offspring vocalisation rate during a social isolation test and participation in a T-maze test. However, no effect of maternal diet was found on layer offspring behaviour. We found several effects of strain on behaviour in the layers. White chickens participated more in T-maze tests as chicks and were likelier to reach the learning criteria in both a T-maze test and discrimination learning task when tested as pullets and adults. Brown chicks vocalised more during social isolation, whereas white chicks spent more time motionless. In a novel object test, brown chickens were observed more frequently on elevated platforms than white chickens indicating greater avoidance of the novel object. We suggest further exploration into the optimal n-6 to n-3 FA ratios for poultry diets using diets closer to the 1:1 ratio found in wild precocial birds. Natural Sciences and Engineering Research Council in Canada, O & T Farms Ltd., Alltech, Ontario Agri-Food Innovation Alliance and Egg Farmers of Canada.

Marek’s disease virus (MDV), avian leukosis virus (ALV), and reticuloendotheliosis virus (REV) are important viral agents associated with neoplastic diseases that cause economic losses for the poultry industry worldwide. Immunosuppressive agents such as infectious bursal disease virus (IBDV), REV, and chicken anemia virus (CIAV) expose birds to other infections and reduce production performance. In this context, we aimed to identify and perform molecular analysis of the aforementioned viral infections (ALV, CIAV, IBDV, MDV, and REV) in the tissues of tumor-bearing chickens. Clinical samples were taken from 11 chicken flocks of different ages and races from some provinces (Adıyaman, Diyarbakır, Elazığ and Malatya) in Turkey between 2011 and 2020. MDV positivity was determined in all 11 chicken flocks, while ALV endogenous sequences were determined in two of 11 MDV positive chicken flocks. CIAV and ALV sequences were found together in two of 11 MDV positive chicken flocks. The ALV subgroup J, IBDV, and REV were not detected in any of the chicken flocks. According to phylogenetic analysis, Turkish MDV strains obtained from this study were included in two different genogroups (genogroups I and II) with other MDV strains with pathotypes ranging from virulent (v) to very virulent plus (vv+). Co-infections of ALV and CIAV with MDV may worsen the current clinical situation. In this study, MDV was detected in two flocks vaccinated with HVT. Other chickens were not vaccinated against any of the viral agents studied. Increasing vaccination and preventive measures against these viral pathogens in poultry in Turkey is recommended.

Engineering of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) system has enabled versatile applications of CRISPR beyond targeted DNA cleavage. Combination of nuclease-deactivated Cas9 (dCas9) and transcriptional effector domains allows activation (CRISPRa) or repression (CRISPRi) of target loci. To demonstrate the effectiveness of the CRISPR-mediated transcriptional regulation in chickens, three CRISPRa (VP64, VPR, and p300) and three CRISPRi (dCas9, dCas9-KRAB, and dCas9-KRAB-MeCP2) systems were tested in chicken DF-1 cells. By introducing guide RNAs (gRNAs) targeting near the transcription start site (TSS) of each gene in CRISPRa and CRISPRi effector domain-expressing chicken DF-1 cell lines, significant gene upregulation was induced in dCas9-VPR and dCas9-VP64 cells, while significant downregulation was observed with dCas9 and dCas9-KRAB. We further investigated the effect of gRNA positions across TSS and discovered that the location of gRNA is an important factor for targeted gene regulation. RNA sequencing analysis of IRF7 CRISPRa and CRISPRi- DF-1 cells revealed the specificity of CRISPRa and CRISPRi-based targeted transcriptional regulation with minimal off-target effects. These findings suggest that the CRISPRa and CRISPRi toolkits are an effective and adaptable platform for studying the chicken genome by targeted transcriptional modulation.

Primordial germ cells (PGCs) are germline-restricted embryonic cells that form the functional gametes of the adult animal. The use of avian PGCs in biobanking and producing genetically modified birds has driven research on the in vitro propagation and manipulation of these embryonic cells. In avian species, PGCs are hypothesized to be sexually undetermined at an early embryonic stage and undergo differentiation into an oocyte or spermatogonial fate dictated by extrinsic factors present in the gonad. However, chicken male and female PGCs require different culture conditions, suggesting that there are sex-specific differences, even at early stages. To understand potential differences between male and female chicken PGCs during migratory stages, we studied the transcriptomes of circulatory stage male and female PGCs propagated in a serum-free medium. We found that in vitro cultured PGCs were transcriptionally similar to their in ovo counterparts, with differences in cell proliferation pathways. Our analysis also revealed sex-specific transcriptome differences between male and female cultured PGCs, with notable differences in Smad7 and NCAM2 expression. A comparison of chicken PGCs with pluripotent and somatic cell types identified a set of genes that are exclusive to germ cells, enriched in the germplasm, and associated with germ cell development.

Error in author list In the published article, there was an error in the named corresponding authors, and author Anamika Mishra was erroneously excluded. The corrected corresponding author list appears below. Katrina M. Morris* - katrina.morris@roslin.ed.ac.uk; katrina.m.morris345@gmail.com Anamika Mishra* - reach2anamika@yahoo.com The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

Meat and poultry are nutrient-dense sources of protein and typically are recommended as part of an overall healthy diet. The objective was to assess the nutritional impact of removing a serving of meat/poultry in Healthy Dietary Patterns (HDPs) using a similar approach to that used by the USDA for Dietary Guidelines for Americans. Composites of minimally processed and further processed meat and poultry were developed and their nutrient profiles were used to accomplish modeling by removing nutrients of each meat and poultry composite from the HDPs. The removal of a 3 oz (85 g) serving of meat or poultry resulted in decreases (10% or more from baseline) in protein and several key micronutrients including iron, phosphorus, potassium, zinc, selenium, thiamine, riboflavin, niacin, vitamin B6, vitamin B12, and choline as well as cholesterol and sodium in the HDPs, and the decreases were consistent for most nutrients with the removal of either minimally processed (fresh) or further processed meat or poultry and even after adjusting for changes in calories. In conclusion, the results of this dietary modeling study show that the removal of a meat and poultry serving from HDPs resulted in decreases in protein and several key nutrients.

In the egg industry, common reproductive disorders, such as internal laying and egg-bound syndrome, not only reduce egg productivity but also cause deaths in severe cases. In this study, we focused on the oviduct histology of the pathogenesis of internal laying and egg-bound syndrome. We divided the aged laying hens into four groups according to the observation of the abdominal cavity and oviductal lumen: healthy, internal laying, egg-bound, and intercurrent. The percentages of healthy, internal laying, egg-bound, and intercurrent groups were 55%, 17.5%, 15%, and 12.5%, respectively. In all parts of the oviduct (i.e., infundibulum, magnum, isthmus, and uterus), the oviductal epithelium was composed of ciliated epithelial cells and secretory cells. The epithelial region lacking cilia was larger in the entire oviduct of the internal laying, and intercurrent groups than in the healthy group. In the internal laying, egg-bound, and intercurrent groups, significant T-cell infiltration was observed in the lamina propria of the entire oviduct. The morphological alteration of ciliated epithelial cells in the oviducts caused by inflammation may be the underlying cause of the pathogenesis of internal laying and egg-bound syndrome.

(1) Background: MicroRNAs (miRNAs) are involved in a variety of biological processes, such as cell proliferation, cell differentiation, and organ development. Recent studies have shown that plant miRNAs may enter the diet and play physiological and/or pathophysiological roles in human health and disease; however, little is known about plant miRNAs in chickens. (2) Methods: Here, we analyzed miRNA sequencing data, with the use of five Chinese native chicken breeds and six different tissues (heart, liver, spleen, lung, kidney, and leg muscle), and used Illumina sequencing to detect the expression of plant miRNAs in the pectoralis muscles at fourteen developmental stages of Tibetan chickens. (3) Results: The results showed that plant miRNAs are detectable in multiple tissues and organs in different chicken breeds. Surprisingly, we found that plant miRNAs, such as tae-miR2018, were detectable in free-range Tibetan chicken embryos at different stages. The results of gavage feeding experiments also showed that synthetic tae-miR2018 was detectable in caged Tibetan chickens after ingestion. The analysis of tae-miR2018 showed that its target genes were related to skeletal muscle organ development, regulation of mesodermal cell fate specification, growth factor activity, negative regulation of the cell cycle, and regulation of growth, indicating that exogenous miRNA may regulate the development of chicken embryos. Further cell cultures and exogenous miRNA uptake assay experiments showed that synthetic wheat miR2018 can be absorbed by chicken myoblasts. (4) Conclusions: Our study found that chickens can absorb and deposit plant miRNAs in various tissues and organs. The plant miRNAs detected in embryos may be involved in the development of chicken embryos.

Sex-linked phenotypes of late feathering (LF) and early feathering (EF) are controlled by a pair of alleles K and k+. Autosexing based on the feathering rate is widely used in poultry production. It is reported that a tandem duplication of 176,324 base pairs linked to the K locus is responsible for LF expression and could be used as a molecular marker to detect LF chicken. So far, there is no genotyping method that can accurately and stably identify the LF homozygote and heterozygote in all chicken breeds. In the present study, a multiplex PCR test was developed to identify EF, LF homozygote, and heterozygote according to electrophoretic bands and the relative height of the peaks by Sanger sequencing. We tested 413 chickens of six native Chinese breeds with this method. The identification was consistent with the sex and phenotype records of the chickens. Band density analysis was performed, and the results supported our genotyping using the new assay. In order to further verify the accuracy of this test in distinguishing homozygote and heterozygote males, 152 LF males were mated with EF females, and the results of the offspring’s phenotypes were consistent with our expectations. Our results support tandem duplication as molecular markers of LF, and this new test is applicable to all LF chickens associated with tandem duplication.

Salmonella is one of the most important zoonotic pathogens that can cause both acute and chronic illnesses in poultry flocks, and can also be transmitted to humans from infected poultry. The purpose of this study was to investigate the prevalence, antimicrobial resistance, and molecular characteristics of Salmonella isolated from diseased and clinically healthy chickens in Anhui, China. In total, 108 Salmonella isolates (5.66%) were successfully recovered from chicken samples (n = 1908), including pathological tissue (57/408, 13.97%) and cloacal swabs (51/1500, 3.40%), and S. Enteritidis (43.52%), S. Typhimurium (23.15%), and S. Pullorum (10.19%) were the three most prevalent isolates. Salmonella isolates showed high rates of resistance to penicillin (61.11%), tetracyclines (47.22% to tetracycline and 45.37% to doxycycline), and sulfonamides (48.89%), and all isolates were susceptible to imipenem and polymyxin B. In total, 43.52% isolates were multidrug-resistant and had complex antimicrobial resistance patterns. The majority of isolates harbored cat1 (77.78%), blaTEM (61.11%), and blaCMY-2 (63.89%) genes, and the antimicrobial resistance genes in the isolates were significantly positively correlated with their corresponding resistance phenotype. Salmonella isolates carry high rates of virulence genes, with some of these reaching 100% (invA, mgtC, and stn). Fifty-seven isolates (52.78%) were biofilm-producing. The 108 isolates were classified into 12 sequence types (STs), whereby ST11 (43.51%) was the most prevalent, followed by ST19 (20.37%) and ST92 (13.89%). In conclusion, Salmonella infection in chicken flocks is still serious in Anhui Province, and not only causes disease in chickens but might also pose a threat to public health security.

Epigenetic modifications play an important role in regulating animal adaptation to external stress. To explore how DNA methylation regulates the expression levels of related genes during forced molting (FM) of laying hens, the hypothalamus and ovary tissues were analyzed at five periods using Whole-Genome Bisulfite Sequencing. The results show that methylation levels fluctuated differently in the exon, intron, 5′UTR, 3′UTR, promoter, and intergenic regions of the genome during FM. In addition, 16 differentially methylated genes (DMGs) regulating cell aging, immunity, and development were identified in the two reversible processes of starvation and redevelopment during FM. Comparing DMGs with differentially expressed genes (DEGs) obtained in the same periods, five hypermethylated DMGs (DSTYK, NKTR, SMOC1, SCAMP3, and ATOH8) that inhibited the expression of DEGs were found. Therefore, DMGs epigenetically modify the DEGs during the FM process of chickens, leading to the rapid closure and restart of their reproductive function and a re-increase in the egg-laying rate. Therefore, this study further confirmed that epigenetic modifications could regulate gene expression during FM and provides theoretical support for the subsequent optimization of FM technology.

The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as “dwarf”, namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.

Salmonella negatively impacts the poultry industry and threatens animals’ and humans’ health. The gastrointestinal microbiota and its metabolites can modulate the host’s physiology and immune system. Recent research demonstrated the role of commensal bacteria and short-chain fatty acids (SCFAs) in developing resistance to Salmonella infection and colonization. However, the complex interactions among chicken, Salmonella, host–microbiome, and microbial metabolites remain unelucidated. Therefore, this study aimed to explore these complex interactions by identifying the driver and hub genes highly correlated with factors that confer resistance to Salmonella. Differential gene expression (DEGs) and dynamic developmental genes (DDGs) analyses and weighted gene co-expression network analysis (WGCNA) were performed using transcriptome data from the cecum of Salmonella Enteritidis-infected chicken at 7 and 21 days after infection. Furthermore, we identified the driver and hub genes associated with important traits such as the heterophil/lymphocyte (H/L) ratio, body weight post-infection, bacterial load, propionate and valerate cecal contents, and Firmicutes, Bacteroidetes, and Proteobacteria cecal relative abundance. Among the multiple genes detected in this study, EXFABP, S100A9/12, CEMIP, FKBP5, MAVS, FAM168B, HESX1, EMC6, and others were found as potential candidate gene and transcript (co-) factors for resistance to Salmonella infection. In addition, we found that the PPAR and oxidative phosphorylation (OXPHOS) metabolic pathways were also involved in the host’s immune response/defense against Salmonella colonization at the earlier and later stage post-infection, respectively. This study provides a valuable resource of transcriptome profiles from chicken cecum at the earlier and later stage post-infection and mechanistic understanding of the complex interactions among chicken, Salmonella, host–microbiome, and associated metabolites.

Spexin2 (SPX2), a paralog of SPX1, is a newly identified gene in non-mammalian vertebrates. Limited studies in fish have evidenced its important role in food intake and energy balance modulation. However, little is known about its biological functions in birds. Using the chicken (c-) as a model, we cloned the full-length cDNA of SPX2 by using RACE-PCR. It is 1189 base pair (bp) in length and predicted to generate a protein of 75 amino acids that contains a 14 amino acids mature peptide. Tissue distribution analysis showed that cSPX2 transcripts were detected in a wide array of tissues, with abundant expression in the pituitary, testis, and adrenal gland. cSPX2 was also observed to be ubiquitously expressed in chicken brain regions, with the highest expression in the hypothalamus. Its expression was significantly upregulated in the hypothalamus after 24 or 36 h of food deprivation, and the feeding behavior of chicks was obviously suppressed after peripheral injection with cSPX2. Mechanistically, further studies evidenced that cSPX2 acts as a satiety factor via upregulating cocaine and amphetamine regulated transcript (CART) and downregulating agouti-related neuropeptide (AGRP) in hypothalamus. Using a pGL4-SRE-luciferase reporter system, cSPX2 was demonstrated to effectively activate a chicken galanin II type receptor (cGALR2), a cGALR2-like receptor (cGALR2L), and a galanin III type receptor (cGALR3), with the highest binding affinity for cGALR2L. Collectively, we firstly identified that cSPX2 serves as a novel appetite monitor in chicken. Our findings will help clarify the physiological functions of SPX2 in birds as well as its functional evolution in vertebrates.

International audience; The chicken chorioallantoic membrane (CAM) is an extraembryonic membrane that is vital for the embryo. It undergoes profound cell differentiation between 11 and 15 days of embryonic incubation (EID), which corresponds to the acquisition of its physiological functions. To gain insight into the functional genes that accompany these biological changes, RNA sequencing of the CAM at EID11 and EID15 was performed. Results showed that CAM maturation coincides with the overexpression of 4225 genes, including many genes encoding proteins involved in mineral metabolism, innate immunity, homeostasis, angiogenesis, reproduction, and regulation of hypoxia. Of these genes, some exhibit variability in expression depending on the chicken breed (broiler versus layer breeds). Besides the interest of these results for the poultry sector, the identification of new functional gene candidates opens additional research avenues in the field of developmental biology.

This study was conducted with the objective of assessing the opportunities and challenges of backyard poultry production at three villages in Ezha district, Gurage Zone of southern Ethiopia using a semi-structured questionnaire, field visit and interview with 150 randomly selected respondents. The dominant chicken production system in the study area was an extensive system (74%) with scavenging and seasonal supplementary feeding (53%). Grains are the main feed used. Almost 65% of poultry share the same room with the main house with perch, the rest 20%, and 15%, respectively, use the different shelters. Most of the farmers (80%) use traditional medicine to treat their chicken. The average age of first laying was 5months, mean number of eggs per clutch was 12. The mean clutch size was 3.3 and the hatchability percentage was 72%. The result revealed that the main constraints of village poultry production in the study area, especially in village2 were predator (48%), disease (33.7%), feed shortage (19.3%), market (10%), and the primary opportunity was extension (34%) followed by credit, (24.6%), market (23.4%) and feed access (18%) and, respectively. It is concluded that constraints and opportunities of village chicken production were identified. Controlling predators, improving the management practices, and educating the framers are viable options to improve the livelihood of the households. &nbsp

A survey of drug combinations employed by the poultry industry indicates that they have played an important role in the control of coccidiosis in chickens. The mode of action of their component drugs is described. Advantages that accrue from their use may include a reduction in potential toxicity, a broadening of their spectrum of activity against different species of Eimeria, activity against different stages of the life cycle, and improved efficacy due to synergism between component drugs. Integration of management procedures involving rotation of drug combinations with vaccination is desirable because this has been shown to result in a restoration of drug sensitivity where drug resistance is present and could contribute to the sustainable control of coccidiosis. Threats to the future use of the most widely used combinations, those that include ionophores, stem from the recent desire to eliminate antibiotics from poultry feeds.

Introduction: Understanding the genetic control of growth traits is essential for effective poultry breeding poultry. One way to identify new loci and confirm existing QTL is through genome-wide association analysis (GWAA) (Wang et al., 2011). In addition, identifying loci with large effects on economically important traits, has been one of the important goal to poultry breeding. QTL assisted selection and genomic regions affecting the production traits have been considered to increase the efficiency of selection and improve production performance (Seabury et al., 2017). Genome wide association studies typically focus on genetic markers with the strongest evidence of association. However, single markers often explain only a small component of the genetic variance and hence offer a limited understanding of the trait under study. A solution to tackle the aforementioned problems, and expand understanding of the genetic background of complex traits, is to move up the analysis from the SNP to the gene and gene-set levels (Peñagaricano et al., 2013). In a gene-set analysis, a group of related genes that harbor significant SNP previously identified in GWAS, is tested for over-representation in a specific pathway. Material and methods: The aim of the this study was to genome wide association studies (GWAS) based on Gene set enrichment analysis for identifying the loci associated with related to body weight and shank length and diameter traits in advanced intercross line (AIL) using the high-confidence SNPs that enable us to study 161376 SNP markers simultaneously. For this purpose, the 599 advanced intercross line and 161376 markers were performed with mixed linear model (MLM) approach was used for the GWAS of the F9 generation, as implemented in the GCTA package (v1.92) (Yang et al., 2011) and no any correction to adjust the error rate. The gene set analysis consisted of three different steps: (1) the assignment of SNPs to genes, (2) the assignment of genes to functional categories, and (3) the association analysis between each functional category and the phenotype of interest. In brief, for each trait, nominal P-values < 0.005 from the GWAS analyses were used to identify significant SNP. Using the biomaRt R package, the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 15 kb up- and downstream of the gene, to include SNP located in regulatory regions. For the assignment of the genes to functional categories, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases were used. The GO database designates biological descriptors to genes based on attributes of their encoded products and it is further partitioned into 3 components: biological process, molecular function, and cellular component. The KEGG pathway database contains metabolic and regulatory pathways, representing the actual knowledge on molecular interactions and reaction networks. Finally, a Fisher’s exact test was performed to test for overrepresentation of the significant genes for each gene-set. The gene enrichment analysis was performed with the goseq R package. In the next step, a bioinformatics analysis was implemented to identify the biological pathways performed in BioMart, Panther, DAVID and GeneCards databases. Results and discussion: Gene set enrichment analysis has proven to be a great complement of genome-wide association analysis (Abdalla et al., 2016). Among available gene set databases, GO is probably the most popular, whereas KEGG is a relatively new tool that is gaining ground in livestock genomics (Morota et al., 2015, 2016). We had hypothesized that the use of gene set information could improve prediction. However, neither of the gene set SNP classes outperformed the standard whole-genome approach. Gene sets have been primarily developed using data from model organisms, such as mice and flies, so it is possible that some of the genes included in these terms are irrelevant for meat production. It is likely that a better understanding of the biology underlying meat production specifically, plus an advance in the annotation of the chicken genome, can provide new opportunities for predicting production using gene set information. Eleven SNP markers on chromosomes 1, 2, 4, 5, 7, 8, 10, 11, and 27 located in MSTN, CAPN3, PNPLA3, ANXA2, IGF1, LDB2, LEPR, FN1, ¬TMEM135, MC4R, EDN1, and ADAMTS18 genes were identified. Some of the genes found to be consistent with some previous studies. Those seem to be involved in biological pathways related to muscle skeletal growth, energy metabolism and bone growth and development. According to pathway analysis, 19 pathways from gene ontology and KEGG pathway were associated with the body weight, shank length and diameter trait (P˂0.05). Among those pathways, the regulation of muscle organ development, regulation of cell growth and anatomical structure homeostasis biological pathway have important roles in the growth and skeletal muscle development. Also, the anatomical structure formation involved in morphogenesis, positive regulation of ossification and calcium signaling pathway presumably has significant association with body weight and shank length as well as diameter traits. Some of these regulatory regions, such as enhancers, are located far from the genes. Therefore, although the gene might be part of the analysis, the relevant variant would probably not be included in the gene set SNP class. Finally, linkage disequilibrium interferes with the use of biological information in prediction because irrelevant regions (regions without any biological role) capture part of the information encoded in relevant regions, causing both regions to exhibit similar predictive abilities. The use of very high density SNP data or even whole genome sequence data could alleviate some of these issues. Finally, it is worth noting that our gene-set enrichment analysis was conducted using a panel of SNP obtained from a single marker regression GWAS, which relies on a simplified theory of the genomic background of traits, without considering for instance the joint effect of SNP. Hence, other approaches (e.g., GWAS exploring SNP by SNP interactions) might provide a better basis for biological pathway analysis. Conclusion: Our observations agreed with the previous results from GWAS of body weight, shank length and diameter traits. Moreover, additional regions in the chicken genome associated with economically important traits were revealed. Our findings would contribute to a better understanding of the genetic control of growth traits in broiler chicken accelerating the genetic progress in poultry breeding programs.

Many behavioral studies and histological analyses of the sense of taste have been conducted in chickens, as it plays an important role in the ingestion of feed. In recent years, various taste receptors have been analyzed, and the functions of fatty acids, umami, and bitter taste receptors in chickens have become clear. In this review, the bitter taste sense in chickens, which is the taste quality by which animals reject poisons, is discussed among a variety of taste qualities. Chickens have taste buds in the palate, the base of the oral cavity, and the root of the tongue. Bitter taste receptors, taste receptor type 2 members 1, 2, and 7 (T2R1, T2R2, and T2R7) are expressed in these tissues. According to functional analyses of bitter taste receptors and behavioral studies, T2R1 and T2R7 are thought to be especially involved in the rejection of bitter compounds in chickens. Furthermore, the antagonists of these two functional bitter taste receptors were also identified, and it is expected that such antagonists will be useful in improving the taste quality of feed materials and poultry drugs that have a bitter taste. Bitter taste receptors are also expressed in extra-oral tissues, and it has been suggested that gastrointestinal bitter taste receptors may be involved in the secretion of gastrointestinal hormones and pathogen defense mechanisms. Thus, bitter taste receptors in chickens are suspected to play major roles in taste sensing and other physiological systems.

Japanese indigenous chickens include approximately 50 breeds exhibiting various morphological traits, such as a long tail. These genetic resources will be important for revealing the genetic basis of morphological traits in the future. However, little is known about the phenotypic characteristics of each breed during the growth stages. To understand age-dependent changes in growth and morphological traits, we investigated tail length, tail number, body weight, and shank length at several time points using three genetically distinct Japanese indigenous chicken breeds. A total of 155 birds from the Tosa-jidori, Chabo, and Minohikichabo breeds were used for trait measurements from 1 to 36 weeks of age to reveal breed and sex effects. Significant sex differences through the growth stages were observed for all traits except for tail number. Although there were no clear breed differences in tail length traits at the 6- and 20-week stages, Minohikichabo ultimately had a significantly longer tail due to extended tail feather growth at later stages (28 and 36 weeks). By measuring two tail length variables (central and maximum), it was revealed that the shape of the tail feathers varies with the growth stage. Minohikichabo's tail number was higher than that of Tosajidori and Chabo at earlier ages (8 and 16 weeks), which leads to an elegant visual in Minohikichabo. Tosa-jidori's body weight was higher than that of Chabo and Minohikichabo, whereas the shank lengths of Chabo and Minohikichabo were shorter than those of Tosa-jidori. These differences in body weight and shank length were consistent from the early to late growth stages. These results revealed the age-dependency of growth and morphological trait breed characteristics.

The aim of this study is to determine the effects of using emulsion manufactured with soybeans (ES) to substitute chicken breast in Vienna sausages. Four types of Vienna sausages (S1: 10% ES and 50% chicken, S2: 20% ES and 40% chicken, S3: 30% ES and 30% chicken, and S4: 40% ES and 20% chicken) for this study were made. The pH, color, proximate composition, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), microphotographs, cooking yields, and texture profile analysis of sausages were examined. The pH value of uncooked and cooked sausages increased significantly with increasing ES content (p

Toll-like receptors (TLRs), as a part of innate immunity, plays an important role in detecting pathogenic molecular patterns (PAMPs) which are structural components or product of pathogens and initiate host defense systems or innate immunity. Precise negative feedback regulations of TLR signaling are important in maintaining homeostasis to prevent tissue damage by uncontrolled inflammation during innate immune responses. In this study, we identified and characterized the function of the pancreatic progenitor cell differentiation and proliferation factor (PPDPF) as a negative regulator for TLR signal-mediated inflammation in chicken. Bioinformatics analysis showed that the structure of chicken PPDPF evolutionarily conserved amino acid sequences with domains, i.e., SH3 binding sites and CDC-like kinase 2 (CLK2) binding sites, suggesting that relevant signaling pathways might contribute to suppression of inflammation. Our results showed that stimulation with polyinosinic:polycytidylic acids (Poly [I:C]), a synthetic agonist for TLR3 signaling, increased the mRNA expression of PPDPF in chicken fibroblasts DF-1 but not in chicken macrophage-like cells HD11. In addition, the expression of pro-inflammatory genes stimulated by Poly(I:C) were reduced in DF-1 cells which overexpress PPDPF. Future studies warrant to reveal the molecular mechanisms responsible for the anti-inflammatory capacity of PPDPF in chicken as well as a potential target for controlling viral resistance.

IntroductionHighly pathogenic avian influenza (HPAI) viruses, such as H5N1, continue to pose a serious threat to animal agriculture, wildlife and to public health. Controlling and mitigating this disease in domestic birds requires a better understanding of what makes some species highly susceptible (such as turkey and chicken) while others are highly resistant (such as pigeon and goose). Susceptibility to H5N1 varies both with species and strain; for example, species that are tolerant of most H5N1 strains, such as crows and ducks, have shown high mortality to emerging strains in recent years. Therefore, in this study we aimed to examine and compare the response of these six species, to low pathogenic avian influenza (H9N2) and two strains of H5N1 with differing virulence (clade 2.2 and clade 2.3.2.1) to determine how susceptible and tolerant species respond to HPAI challenge.MethodsBirds were challenged in infection trials and samples (brain, ileum and lung) were collected at three time points post infection. The transcriptomic response of birds was examined using a comparative approach, revealing several important discoveries.ResultsWe found that susceptible birds had high viral loads and strong neuro-inflammatory response in the brain, which may explain the neurological symptoms and high mortality rates exhibited following H5N1 infection. We discovered differential regulation of genes associated with nerve function in the lung and ileum, with stronger differential regulation in resistant species. This has intriguing implications for the transmission of the virus to the central nervous system (CNS) and may also indicate neuro-immune involvement at the mucosal surfaces. Additionally, we identified delayed timing of the immune response in ducks and crows following infection with the more deadly H5N1 strain, which may account for the higher mortality in these species caused by this strain. Lastly, we identified candidate genes with potential roles in susceptibility/resistance which provide excellent targets for future research.DiscussionThis study has helped elucidate the responses underlying susceptibility to H5N1 influenza in avian species, which will be critical in developing sustainable strategies for future control of HPAI in domestic poultry.

The oil cakes of essential oil plants were screened for prebiotic properties for further development of prebiotic feeds for livestock animals based on these essential oil plants’ extracts. For screening, a microbiota model of the chicken cecum, which was created on the basis of an artificial intestinal medium, was used. This model renders it possible to simulate conditions close to intestinal ones. Oligofructose, inulin, β-glucan, psyllium seeds, and apple fiber at a concentration of 0.5% were used as substances with known prebiotic properties. The oil cake concentration was 0.5%, 1%, 2%, and 4%. The direct antimicrobial effect of the cakes on intestinal bacteria was also investigated. The ability of the cakes to stimulate a decrease in the pH level by Lactobacillus was studied under conditions close to intestinal ones. It was shown that the cakes of big seed false flax (Camelina sativa), brown mustard (Brassica juncea), and spicate lavender (Lavandula angustifolia) exhibit prebiotic properties in relation to the microbiome of chickens in model experiments. They enhance the acid-forming properties of lactic acid bacteria, thereby lowering the pH of the medium. This leads to a decrease in the number of Enterococcus, Escherichia coli, and lactose-positive bacteria, as well as a complete suppression of Proteus. The optimal oil cake concentrations are 1% and 2%. These oil cakes are promising sources of prebiotics for the development of prebiotic feed for agriculture.

As previously reported, inflammatory activity initiated by intradermal injection of multiple growing feather (GF)-pulps of a chicken with lipopolysaccharide, and the subsequent periodic sampling of GFs and blood, enables the longitudinal evaluation of in vivo tissue- and systemic-inflammatory activities by ex vivo laboratory analyses. To demonstrate the suitability of this two-window approach to monitor and assess vaccine responses, two groups of chickens were immunized by intramuscular injection of mouse IgG (mIgG), mIgG in alum adjuvant (Alum&mIgG), or PBS-vehicle (Group I and II at 7- and 7- and 11-weeks, respectively). Plasma levels of mIgG-specific antibodies were monitored by ELISA for 28 days post-primary- and secondary-immunizations. To examine the cellular responses, 20 GF-pulps per bird were injected with mIgG on Day-10 or Day-5 post-primary- or -secondary-immunization, respectively. Two GFs were collected before- and at various times (0.25 to 7 days) post-injection for leukocyte population- and cytokine mRNA expression-analyses. The observed primary- and secondary-antibody response profiles were as expected for a T-dependent antigen. Leukocyte- and cytokine-profiles established in GF-pulps revealed temporal, qualitative, and quantitative differences in local naïve, primary, and secondary leukocyte-effector responses to antigen. This study demonstrates the unique opportunity in the avian model to monitor both cell- and antibody-mediated immune responses using minimally invasive techniques.

Evidence suggests that susceptibility to avian influenza A virus in chickens is influenced by host genetics, but the mechanisms are poorly understood. A previous study demonstrated that inbred line 0 chickens are more resistant to low-pathogenicity avian influenza (LPAI) infection than line CB.12 birds based on viral shedding, but the resistance was not associated with higher AIV-specific IFNγ responses or antibody titres. In this study, we investigated the proportions and cytotoxic capacity of T-cell subpopulations in the spleen and the early immune responses in the respiratory tract, analysing the innate immune transcriptome of lung-derived macrophages following in vitro stimulation with LPAI H7N1 or the TLR7 agonist R848. The more susceptible C.B12 line had a higher proportion of CD8αβ+ γδ and CD4+CD8αα+ αVβ1 T cells, and a significantly higher proportion of the CD8αβ+ γδ and CD8αβ+ αVβ1 T cells expressed CD107a, a surrogate marker of degranulation. Lung macrophages isolated from line C.B12 birds expressed higher levels of the negative regulator genes TRIM29 and IL17REL, whereas macrophages from line 0 birds expressed higher levels of antiviral genes including IRF10 and IRG1. After stimulation with R848, the macrophages from line 0 birds mounted a higher response compared to line C.B12 cells. Together, the higher proportion of unconventional T cells, the higher level of cytotoxic cell degranulation ex vivo and post-stimulation and the lower levels of antiviral gene expression suggest a potential role of immunopathology in mediating susceptibility in C.B12 birds.

Enteroids are miniature self-organising three-dimensional (3D) tissue cultures which replicate much of the complexity of the intestinal epithelium. We recently developed an apical-out leukocyte-containing chicken enteroid model providing a novel physiologically relevant in vitro tool to explore host–pathogen interactions in the avian gut. However, the replicate consistency and culture stability have not yet been fully explored at the transcript level. In addition, causes for the inability to passage apical-out enteroids were not determined. Here we report the transcriptional profiling of chicken embryonic intestinal villi and chicken enteroid cultures using bulk RNA-seq. Comparison of the transcriptomes of biological and technical replicate enteroid cultures confirmed their high level of reproducibility. Detailed analysis of cell subpopulation and function markers revealed that the mature enteroids differentiate from late embryonic intestinal villi to recapitulate many digestive, immune and gut-barrier functions present in the avian intestine. These transcriptomic results demonstrate that the chicken enteroid cultures are highly reproducible, and within the first week of culture they morphologically mature to appear similar to the in vivo intestine, therefore representing a physiologically-relevant in vitro model of the chicken intestine.