Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Probiotic-induced differential gene expression during Salmonella challenge in neonatal chicks

ABSTRACT: Salmonella remains an important enteric pathogen of poultry, primarily due to concerns regarding food-borne illness in humans consuming contaminated poultry products. Specific probiotic cultures are efficacious as a treatment for neonatal poultry to prevent enteric infections (competitive exclusion) due to the exquisite susceptibility of young chicks to pathogens in the hatchery and brooding environment. The objective of this experiment was to analyze transcriptional profiles in the ceca of neonatal chicks using the Arizona Gallus gallus 20.7K Oligo Array v1.0, following treatment with a probiotic culture derived from poultry with and without Salmonella enterica subsp. Enteritidis (SE) challenge. Chicks were obtained from a commercial hatchery, and challenged with SE upon arrival at the laboratory. One hour post-challenge, chicks were treated with a probiotic culture (FM-B11). Treatment groups included: Control (no challenge or treatment, vehicle only), SE (challenged only), B11 (treated only) and SE+B11 (challenged and treated). Samples were obtained at 12h and 24h post-treatment. We observed that administration of a Lactobacillus-based probiotic culture to chicks following challenge with SE reduced SE colonization of the cecae and resulted in differential expression of genes in the cecae. Among all four treatment groups, 309 genes were differentially expressed (p<0.05) at 12h, and 352 genes were differentially expressed (p<0.05) at 24h. Keywords: disease state analysis Eight experimental groups with 4 replicates each were analyzed. A reference RNA design was used for this microarray. Equal amounts of amplified RNA (aRNA) from all samples were pooled and labelled with the Alexa 647 to create the reference pool. Each individual sample was labelled with Alexa 555. Each slide was hybridized with both the reference pool and one sample.

ORGANISM(S): Gallus gallus

SUBMITTER: T Porter

PROVIDER: E-GEOD-19887 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Delayed access to feed following hatching has been associated with reduction in growth performance in chicks. However, the gene networks within the hypothalamus that regulate feed intake and metabolism, and the effects of fasting on those pathways are not well understood. The present experiment evaluated global hypothalamic gene expression in neonatal chicks using the Arizona Gallus gallus 20.7K Oligo Array v1.0 to elucidate genes and pathways regulated by feeding, fasting, and refeeding. Ten groups of chicks were sampled over four days post-hatch, including: control (at hatch), 24h fed, 24h fasted, 48h fed, 48h fasted, 48h fasted then 4h refed, 72h fed, 48h fasted then 24h refed, 96h fed, and 48h fasted then 48h refed. Non-esterified fatty acids were elevated, and triglycerides were decreased in fasted chicks at 24 and 48h, indicating that fasting induced physiological changes. Hypothalamic samples were collected from 16 chicks per group, and total RNA was extracted and pooled for hybridization (n=4). Expression patterns of selected genes were confirmed by quantitative real-time PCR. Two-fold differences in gene expression were detected in 1,272 genes between treatment groups, and of those, 119 genes were significantly (P<0.05) different. Assignment of gene ontology terms to the significant genes resulted in 34 different categories of biological processes, with 24% of genes participating in signal transduction, transport, or metabolic processes. Genes that were upregulated during fasting (and confirmed by qPCR) include FK506BP51, which is involved in the formation of steroid receptor complexes, and deiodinase type II, which is responsible for converting the thyroid hormone T4 into T3. Confirmed genes, downregulated due to fasting, included proopiomelanocortin and fatty acid binding protein 7. Other regulated genes were identified that play a role in feeding and obesity in other species, such as relaxin 3 and adrenergic receptor-β2. Further analysis of differentially regulated genes could provide new information regarding the role of the hypothalamus in feed intake and metabolism. Keywords: Metabolic perturbation Ten experimental groups with 4 replicates each were analyzed. A reference RNA design was used for this microarray. Equal amounts of amplified RNA (aRNA) from all samples were pooled and labeled with the Alexa 647 to create the reference pool. Each individual sample was labeled with Alexa 555. Each slide was hybridized with both the reference pool and one sample.

Project description:This study integrates global transcriptional profiling and the metabolic perturbation induced by fasting and re-feeding. Genetic control of growth and development should be revealed by systematic modeling of metabolic and regulatory pathways. Chicken oligo arrays were used for transcriptional profiling in two time-course experiments. Two critical developmental stages were chosen: immediately after hatchling (Wk1) and prior to marketing of broiler chickens (Wk6). Only male chickens were used to simplify the experimental design. A RNA reference design was employed for microarray hybridization using two reference RNA pools derived from all individuals sampled at either Wk1 or Wk6. Microarray data was acquired using GenePix Pro software. Loess normalization and a linear mixed model were applied in data processing using the R statistical package with LIMMA software [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3]. The results show hundreds of differentially expressed genes, which are regulated by age and the metabolic perturbation of fasting and re-feeding. Numerous common genes were found at both developmental stages (Wk1 and Wk6) that could be candidates for controlling growth and development of chickens. Differential expression revealed by either microarray or qRT-PCR analyses of selected genes was highly consistent. QRT-PCR verification of genes acutely depressed by fasting includes AGO1, ANGTPL3, ATPCL, FASN, FAT, ME1, PPARG, SCD1, SREBP1 and THRSPA. Genes up-regulated by fasting were ALDOB, IL-15, LDHB, LIPIN2, PANK1, PPARA and UPP2. These genes are functionally assigned to metabolic enzymes, transcription factors, acute phase proteins, immune factors and involved in various pathways (i.e., fatty acid and amino acid metabolism, glycolysis, growth factor signaling and immune defense). A reference RNA design was used for microarray hybridizations, where the same reference RNA pool was co-hybridized to each target sample on an microarray. The reference RNA pool was made from an equal amount of high-quality amplified RNA (aRNA), derived from all liver samples within each experiment (Wk1 = 50 samples and Wk6 = 30 samples). The reference RNA pool was labeled with Alexa 647 while each target sample was labeled with Alexa 555.

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Probiotic-induced differential gene expression during Salmonella challenge in neonatal chicks

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