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RNA-Seq analysis of broiler intestinal transcriptome reveals new insight on the interaction between antibiotic growth promoters (AGPs) and the host

ABSTRACT: Purpose: Identify at the transcriptome level genes that could be involved in the mode of action of avilamycin, an AGP, when administered at non-therapeutic concentrations, and use this information in regard to development of alternatives to AGPs. Methods: Out of 120 broiler chickens fed either CONTROL feed or AGP feed (supplemented with avilamycin; Surmax® 100, 10 g/1000 kg of feed, Elanco), the RNA from the ileum tissue of five birds per group was isolated from day 35, profiled by RNA-sequencing, and results were verified via RT-qPCR. Results: Overall, 66 differentially expressed genes (DEGs; FDR ≤ 0.05 and fold change ≥ 2 or ≤ -2) were found in the ileum of chicken fed avilamycin in comparison to the control group. Only partial agreement was found on the DEGs (64%) when the reads were initially mapped to the former genome assembly Galgal5 instead of GRCg6a. Functional enrichment analysis showed that the down-regulated DEGs were associated with signaling by interleukins, and that IL-22 and certain antimicrobial peptides could play a central role in the intestinal host response to avilamycin at day 35. This was further corroborated on sixteen chickens per group via RT-qPCR. In addition, higher activity was detected in module of genes related to lipid metabolism and transport in the avilamycin group, as revealed by the co-expression network analysis. Conclusions: Improved feed efficiency was correlated with reduced immunological stress in the intestinal mucosa. The RNA-Seq approach allowed generating novel knowledge that could contribute to the development of AGP alternatives, with IL-22 identified as a potential marker.

ORGANISM(S): Gallus gallus

PROVIDER: GSE135272 | GEO | 2020/12/31

REPOSITORIES: GEO

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Project description:Eimeria (E.) maxima parasite infects the midgut disrupting the jejunal and ileal mucosal lining causing high morbidity and mortality in chickens. Heat stress (HS) is a seasonal stressor that affects biological functions leading to poor performance. Our objective was to elucidate how HS, E. maxima infection, and their combination affect the ileum transcriptome. Two-hundred and forty 2-week-old males Ross708 chickens were randomly allocated into four treatment groups: thermoneutral control (TNc), thermoneutral infected (TNi), heat stress control (HSc), and heat stress infected (HSi), with 6 replicates each of 10 birds. Infected groups received 200x103 sporulated E. maxima oocysts/bird, and heat treatment groups were raised at 35oC. At 6-day post-treatment, five chickens per group were randomly sampled, and ileum tissues were collected for RNA extraction and sequencing using NGS Illumina sequencing platforms. A total of 413, 3377, 1908, and 2304 DEGs were identified when applying the comparisons: TNc vs HSc, TNc vs TNi, HSi vs HSc, and TNi vs HSi, respectively, at cutoff ≥1.2-fold change (FDR: q<0.05). HSc vs TNc showed upregulation of lipid metabolic pathways and degradation and metabolism of multiple amino acids, and downregulation of most immune-related and protein synthesis pathways. TNc vs TNi displayed upregulation of most of the immune-associated pathways and eukaryotic mRNA maturation pathways, and downregulation of fatty acid metabolism and multiple amino acid metabolism pathways including tryptophan. Comparing HSi versus HSc and TNi revealed that combining the two stressors restored some normal cellular functions, e.g., oxidative phosphorylation and protein synthesis, and reduced the intensity of immune response associated with E. maxima infection. Tryptophan metabolism was upregulated, including genes that contribute to catabolizing tryptophan through serotonin and indole pathways; which might result in reducing the cytoplasmic pool of nutrients and calcium available for the parasite to scavenge and consequently might affect the parasite’s reproductive ability.

Project description:As an essential micronutrient for animals, vitamin E plays crucial physiological roles in reproduction, antioxidant and immune functions, and lipid metabolism. The objective of this study was to reveal molecular mechanism of vitamin E on intramuscular fat (IMF) deposition through transcriptome sequencing of pectoral muscle in broiler chickens. A total of 240 one-day-old health female chicks were randomly allocated into five dietary treatments with each treatment six replicates. The birds were fed basal diet supplemented with 0 and 100 IU/kg vitamin E in the form of DL-α-tocopheryl acetate, respectively. The body weight, carcass performance and IMF content were measured. Transcriptome profile of pectoral muscle in 35-day-old chickens were sequencing from the control and 100 IU/kg vitamin E treatment. Functional enrichment analyzes of differentially expressed genes (DEGs) based on Gene ontology (GO), KEGG pathway and bio function, and network were performed. Results shown that IMF content of broiler chickens were significantly increased at 12.89% (P < 0.05) between 100 IU/kg vitamin E treatment and control. Transcriptome sequencing results for pectoralis major muscle of 100 IU vitamin E-supplemented and the control groups identified 57 up-regulated and 102 down-regulated DEGs. These DEGs were significantly enriched (FDR corrected P-value < 0.05) in 13 of 236 GO terms involved in muscle development- and lipid metabolism. Pathway functional enrichment analysis revealed that the DEGs were significantly enriched in three signalling pathways (FDR corrected P-value < 0.05). Two of them, MAPK signaling pathway and FoxO signaling pathway, play key roles in muscular and lipid metabolism. It is worth mentioning that 46 DEGs were significantly enriched in 28 skeletal and muscular system development and function categories and 31 DEGs were significantly enriched in 17 lipid metabolism function categories. Moreover, three lipid metabolism and muscular development-related networks of DEGs were also identified. These DEGEs, pathways, function categories and networks identified in this study provide us new insights for the vitamin E regulation of the IMF deposition in broiler chickens.

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RNA-Seq analysis of broiler intestinal transcriptome reveals new insight on the interaction between antibiotic growth promoters (AGPs) and the host

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