Differences in intestinal gene expression profiles in broiler lines varying in susceptibility to malabsorption syndrome

Growth performance, behavior, gene expression, carcass characteristics, stress indicators, and economical parameters of avian 48 broiler chickens raised under three different stocking density

The current research evaluated the consequence of varying stocking densities on growth performance, carcass features, hematological, welfare, economic parameters, and immune markers of broiler chicks. A total of 324 Avian 48 were haphazardly classified into three different stocking densities. There were 14 birds/m2 in the low stocking density (LSD) group, 18 birds/m2 in the medium stocking density (MSD) group, and 22 in the high stocking density (HSD) group. Compared to the other two groups, the HSD birds' body weight and daily weight gain were significantly lower (p < 0.05). The LSD group demonstrated a significant increase in productive efficiency (EPEF and EBI) compared to the medium and high SD groups (p < 0.003). The birds from the HSD group exhibited the lowest values for carcass characteristics compared to the low and medium SD groups. At the hematological level, the HSD group exhibited significantly elevated levels of HB, RBCs, heterophils, and lymphocytes compared to the LSD and MSD groups (p < 0.011, p < 0.0001, and p < 0.0001), respectively. Compared to the LSD group, the levels of cortisol, a hallmark of oxidative stress, were considerably greater in the MSD and HSD groups (p < 0.0001). Concerning gene expression, the birds in the LSD group exhibited a significant improvement in growth, intestinal health, and anti-inflammatory genes compared to the MSD and HSD groups. In addition, inflammatory markers were significantly downregulated. The HSD group exhibited the lowest net profit compared to the other groups (p < 0.0001). At the behavioral level, birds in the LSD group demonstrated a significantly shorter TI duration (p < 0.0001) and latency (p < 0.043) in OFT to the first step, lower mobility duration (p < 0.004), and pecking (p < 0.05) compared to other groups. Our study concluded that rearing in LSD up to MSD could be applied without compromising broiler performance.

Gene expression profiles of the small intestine of village chickens from an Ascaridia galli infested environment

•

The transcriptome of chickens from parasite infested environment was sequenced.

•

Different genes were reported between A. galli infected and non-infected chickens.

•

Upregulated immune and inflammatory response genes are associated with fighting parasites.

•

T cell receptor signalling and arachidonic acid metabolism pathways were impacted.

•

Different segments of the intestines differed in gene expression and associated pathways.

Nematodes of the genus Ascaridia are known to infect many species of birds and result in fatal diseases. A. galli damages the intestinal mucosa of chickens leading to blood loss, secondary infection and occasionally the obstruction of small intestines due to high worm burden. This study investigated the gene expression profiles in chickens from two different provinces of South Africa naturally exposed to A. galli infestations and tested either positive or negative for the parasite. The study further investigated gene expression profiles of the A. galli infected duodenum, jejunum and ileum tissues of the small intestines. The A. galli positive intestines displayed hypertrophy of the intestinal villi with accumulation of inflammatory cells and necrosis of the crypts of Lieberkühn glands, lesions that were absent in the uninfected intestines. Total RNA isolated from small intestines of infected and non-infected intestines was sequenced using Illumina HiSeq technology to generate up to 23,856,130 reads. Between any two-way comparisons of the intestines, 277 and 190 transcripts were significantly expressed in Limpopo and KwaZulu-Natal (KZN) chickens, respectively. Gene ontology analysis of the differentially expressed genes (DEGs) revealed an enrichment of genes reported to function in the immune response, defense response, inflammatory response and cell signalling genes. T cell receptor signalling pathways and arachidonic acid metabolism pathways were among the most significantly impacted pathways. Overall, the study provided insights into adaptative mechanisms for chickens extensively raised in parasite infected environments.

A Systematic Analysis on mRNA and MicroRNA Expression in Runting and Stunting Chickens

Runting and stunting syndrome (RSS), which is characterized by lower body weight, widely occurs in broilers. Some RSS chickens simply exhibit slow growth without pathological changes. An increasing number of studies indicate that broiler strains differ in susceptibility to infectious diseases, most likely due to their genetic differences. The objective of this study was to detect the differentially expressed miRNAs and mRNAs in RSS and normal chickens. By integrating miRNA with mRNA expression profiling, potential molecular mechanisms involved in RSS could be further explored. Twenty-two known miRNAs and 1,159 genes were differentially expressed in RSS chickens compared with normal chickens (P < 0.05). qPCR validation results displayed similar patterns. The differentially expressed genes were primarily involved in energy metabolism pathways. The antisense transcripts were extensively expressed in chicken liver albeit with reduced abundance. Dual-luciferase reporter assay indicated that gga-miR-30b/c directly target CARS through binding to its 3′UTR. The miR-30b/c: CARS regulation mainly occurred in liver. In thigh muscle and the hypothalamus, miR-30b/c are expressed at higher levels in RSS chickens compared with normal chickens from 2 to 6 w of age, and notably significant differences are observed at 4 w of age.

Morphometric evaluation of "dysbacteriosis" in broilers

In consequence of the withdrawal of products that assisted animal production, such as antimicrobial growth promoters, once-controlled enteric diseases have returned and new multifactorial diseases causing gut disorders of unknown origin have emerged in broilers. One of these widespread syndromes causing intestinal health problems in broilers is in the field referred to as "dysbacteriosis". During the present study, the histopathology of the intestinal tract of broilers affected with dysbacteriosis was analysed. Commercial broilers were given a macroscopic dysbacteriosis score by experienced veterinarians during necropsy. Samples from the duodenum and caecum were taken from each broiler for histopathological analysis. An increase in the macroscopic dysbacteriosis score coincided with increased villus atrophy, a decrease in the thickness of the tunica muscularis and an increase in T-lymphocyte infiltration in the gut mucosa. Also more and larger goblet cells were observed in the animals with high macroscopic dysbacteriosis scores. Although the exact aetiology still remains to be identified, dysbacteriosis in broiler chickens thus coincides with an inflammatory reaction in the gut mucosa.

Effect of organically and conventionally produced diets on jejunal gene expression in chickens

Using a nutrigenomics approach we studied the response of second-generation chickens at a transcriptional level to organically grown feed ingredients compared with conventionally grown feed ingredients. Both diets consisted of the same amounts of ingredients, the only difference was the production method. Gene expression was analysed in jejuni using whole genome chicken cDNA arrays. After analysis, forty-nine genes were found to be differentially regulated between chickens fed on the different diets, independent of their genetic background. Of these forty-nine genes, seven genes were involved in cholesterol biosynthesis. Genes involved in cholesterol biosynthesis were higher expressed in jejuni from organically fed birds. Other genes found to be regulated were involved in immunological processes, such as B-G protein (part of chicken major histocompatibility complex), chemokine ah221, and the immunoglobulin heavy chain. Using quantitative PCR the effect of genetic background on the differential expression of genes was studied. Differences in gene expression existed between animals fed different diets as well as between different chicken lines. This indicated that diet and genetic background influence the transcriptional response of the jejunum. This is the first time that significant differences in gene expression were shown between animals on diets with organically or conventionally produced ingredients.

Effects of organically and conventionally produced feed on biomarkers of health in a chicken model

Consumers expect organic products to be healthier. However, limited research has been performed to study the effect of organic food on health. The present study aimed to identify biomarkers of health to enable future studies in human subjects. A feeding experiment was performed in two generations of three groups of chickens differing in immune responsiveness, which were fed identically composed feeds from either organic or conventional produce. The animals of the second generation were exposed to an immune challenge and sacrificed at 13 weeks of age. Feed and ingredients were analysed on macro- and micronutrients, i.e. vitamins, minerals, trace elements, heavy metals and microbes. The chickens were studied by general health and immune parameters, metabolomics, genomics and post-mortem evaluation. The organic and conventional feeds were comparable with respect to metabolisable energy. On average, the conventionally produced feeds had a 10 % higher protein content and some differences in micronutrients were observed. Although animals on both feeds were healthy, differences between the groups were found. The random control group of chickens fed conventional feed showed overall a higher weight gain during life span than the group on organic feed, although feed intake was mostly comparable. The animals on organic feed showed an enhanced immune reactivity, a stronger reaction to the immune challenge as well as a slightly stronger 'catch-up growth' after the challenge. Biomarkers for future research were identified in the parameters feed intake, body weight and growth rate, and in immunological, physiological and metabolic parameters, several of these differing most pronounced after the challenge.

Expression profiling of the solute carrier gene family in chicken intestine from the late embryonic to early post-hatch stages

Intestinal development during late embryogenesis and early post-hatch has a long-term influence on digestive and absorptive capacity in chickens. The objective of this research was to obtain a global view of intestinal solute carrier (SLC) gene family member expression from late embryogenesis until 2 weeks post-hatch with a focus on SLC genes involved in uptake of sugars and amino acids. Small intestine samples from male chicks were collected on embryonic days 18 (E18) and 20 (E20), day of hatch and days 1, 3, 7 and 14 post-hatch. The expression profiles of 162 SLC genes belonging to 41 SLC families were determined using Affymetrix chicken genome microarrays. The majority of SLC genes showed little or no difference in level of expression during E18-D14. A number of well-known intestinal transporters were upregulated between E18 and D14 including the amino acid transporters rBAT, y(+)LAT-2 and EAAT3, the peptide transporter PepT1 and the sugar transporters SGLT1, GLUT2 and GLUT5. The amino acid transporters CAT-1 and CAT-2 were downregulated. In addition, several glucose and amino acid transporters that are novel to our understanding of nutrient absorption in the chicken intestine were discovered through the arrays (SGLT6, SNAT1, SNAT2 and AST). These results represent a comprehensive characterization of the expression profiles of the SLC family of genes at different stages of development in the chicken intestine and lay the ground work for future nutritional studies.

Immunological and gene expression responses to a Salmonella infection in the chicken intestine

Besides infection in humans, Salmonella enteritidis can also cause serious illness in young chickens. However, the genetic and immunological parameters important for the disease in chickens are not well characterized. In this study, processes in the chicken intestine in response to a Salmonella infection were investigated in two different chicken lines. One-day-old chickens were orally infected with Salmonella. T-cell subpopulations, phagocytic properties of intestinal mononuclear cells and RNA expression levels of the jejunum were investigated. The two chicken lines differed in the amount of cfu in the liver and growth retardation after the infection. Differences in phagocytic activity of intestinal mononuclear cells were found between control and Salmonella infected chickens. The number of CD4+ T-cells of the intestine decreased after the Salmonella infection in one chicken line, while the number of CD8+ T-cells increased in both chicken lines, but the time post infection of this increase differed between the lines. In one chicken line the expression levels of the genes carboxypeptidase M and similar to ORF2 decreased after the Salmonella infection, which might be related to a decrease in the amount of macrophages. With the microarray, ten genes were found that were regulated in only one of the chicken lines, while we found six genes regulated in response to the infection in both chicken lines. So differences in genetic background of the chickens influence the intestinal host response of the Salmonella infection as observed by phagocytic activity, gene expression and changes in the number of T-cell subpopulations and macrophages.

Gene expression responses to a Salmonella infection in the chicken intestine differ between lines

Poultry products are an important source of Salmonella enterica. An effective way to reduce food poisoning due to Salmonella would be to breed chickens more resistant to Salmonella. Unfortunately host responses to Salmonella are complex with many factors involved. To learn more about responses to Salmonella in young chickens, a cDNA microarray analysis was performed to compare gene expression profiles between two chicken lines under control and Salmonella infected conditions. Newly hatched chickens were orally infected with S. enterica serovar Enteritidis. Since the intestine is the first barrier the bacteria encounter after oral inoculation, intestinal gene expression was investigated at different timepoints. Differences in gene expression between the two chicken lines were found in control as well as Salmonella infected conditions. In response to the Salmonella infection a fast growing chicken broiler line induced genes that affect T-cell activation, whereas in a slow growing broiler line genes involved in macrophage activation seemed to be more affected at day 1 post-infection. At days 7 and 9 most gene expression differences between the two chicken lines were identified under control conditions, indicating a difference in the intestinal development between the two chicken lines which might be linked to the difference in Salmonella susceptibility. The findings in this study have lead to the identification of novel genes and possible cellular pathways, which are host dependent.

Maternal diet influences gene expression in intestine of offspring in chicken (Gallus gallus)

The diet of the mother during pregnancy influences the onset of different diseases and health-related traits in the offspring. We investigated the influence of the mother hen diet on the intestinal gene expression pattern in the offspring. Hens received for 11 weeks either a commercial feed or a commercial feed supplemented with vitamins and minerals. The offspring of the two groups showed no changes in growth rate or feed conversion. Of this offspring, gene expression patterns in the intestine were measured at 3 and 14 days of age with an intestinal cDNA-microarray. Between the two groups, 11 genes were found to be differentially expressed both at 3 and 14 days of age. Thus, these genes were differently regulated when the intestine is developing as well as when the intestine is more mature. Genes that are differentially expressed at day 3 and/or day 14 affect intestinal turnover, proliferation and development, metabolism and feed absorption. To confirm that differences in gene expression are related to intestinal development, we investigated intestinal proliferation. This indeed also showed differences in proliferation between the two groups at day 3 and day 14 of age. The gene expression and proliferation results indicate that feed of the hens influences the functionality of intestine of the offspring at day 3 and 14 of age.

Early host gene expression responses to a Salmonella infection in the intestine of chickens with different genetic background examined with cDNA and oligonucleotide microarrays

So far the responses of chickens to Salmonella have not been studied in vivo on a whole genome-wide scale. Furthermore, the influence of the host genetic background on gene expression responses is unknown. In this study gene expression profiles in the chicken (Gallus gallus) intestine of two genetically different chicken lines were compared, 24 h after a Salmonella enteritidis inoculation in 1-day-old chicks. The two chicken lines differed in the severity of the systemic infection. For gene expression profiles, a whole genome oligonucleotide array and a cDNA microarray were used to compare both platforms. Genes upregulated in both chicken lines after the Salmonella infection had a function in the innate immune system or in wound healing. Genes regulated after the Salmonella infection in one chicken line encoded proteins involved in inflammation, or with unknown functions. In the other chicken line upregulated genes encoded proteins involved in acute phase response, the fibrinogen system, actin polymerisation, or with unknown functions. Some of the host gene responses found in this study are not described before as response to a bacterial infection in the intestine. The two chicken lines reacted with different intestinal gene responses to the Salmonella infection, implying that it is important to use chickens with different genetic background to study gene expression responses.

Recent advances in immunomodulation and vaccination strategies against coccidiosis

Coccidiosis is a ubiquitous intestinal protozoan infection of poultry seriously impairing the growth and feed utilization of infected animals. Conventional disease control strategies rely heavily on chemoprophylaxis, which is a tremendous cost to the industry. Existing vaccines consist of live virulent or attenuated Eimeria strains with limited scope of protection against an ever-evolving and widespread pathogen. The continual emergence of drug-resistant strains of Eimeria, coupled with the increasing regulations and bans on the use of anticoccidial drugs in commercial poultry production, urges the need for novel approaches and alternative control strategies. Because of the complexity of the host immunity and the parasite life cycle, a comprehensive understanding of host-parasite interactions and protective immune mechanisms becomes necessary for successful prevention and control practices. Recent progress in functional genomics technology would facilitate the identification and characterization of host genes involved in immune responses as well as parasite genes and proteins that elicit protective host responses. This study reviews recent coccidiosis research and provides information on host immunity, immunomodulation, and the latest advances in live and recombinant vaccine development against coccidiosis. Such information will help magnify our understanding of host-parasite biology and mucosal immunology, and we hope it will lead to comprehensive designs of nutritional interventions and vaccination strategies for coccidiosis.

Chicken functional genomics: an overview

Chickens have undergone intensive selection to produce highly productive strains with excellent growth rates and feed conversion ratios. There does not appear to be any reduction in the rate of strain improvement. The recently completed chicken genome sequencing project and adjunct projects cataloging single nucleotide polymorphisms demonstrate that there is still a high level of genetic variation present in modern breeds. The information provided by genome and transcriptome studies furnishes the chicken biologist with powerful tools for the functional analysis of gene networks. Gene microarrays have been constructed and used to investigate gene expression patterns associated with certain production traits and changes in expression induced by pathogen challenge. Such studies have the potential to identify important genes involved in biological processes influencing animal productivity and health. Fundamental regulatory mechanisms controlled by non-coding RNAs, such as microRNAs, can now be studied following the identification of many potential genes by homology with previously identified genes from other organisms. We demonstrate here that microarrays and northern blotting can be used to detect expression of microRNAs in chicken tissue. Other tools are being used for functional genomic analysis including the production of transgenic birds, still a difficult process, and the use of gene silencing. Gene silencing via RNA interference is having a large impact in many areas of functional genomics and we and others have shown that the mechanisms needed for its action are functional in chickens. The chicken genome sequence has revealed a large number of immune related genes that had not previously been identified in chickens. Functional analysis of these genes is likely to lead to applications aimed at improving chicken health and productivity.